From d59ecf72d0fbd22bfe2c8d924b637ae6124bbb00 Mon Sep 17 00:00:00 2001 From: Pablo Date: Thu, 16 May 2024 17:09:32 +0200 Subject: [PATCH 01/18] appy changes for ARM Signed-off-by: Pablo --- modules/local/star_align_igenomes/main.nf | 2 +- modules/local/star_genomegenerate_igenomes/main.nf | 2 +- modules/nf-core/bbmap/bbsplit/environment.yml | 2 +- modules/nf-core/bedtools/genomecov/environment.yml | 3 ++- modules/nf-core/bedtools/genomecov/main.nf | 2 +- modules/nf-core/cat/fastq/environment.yml | 2 +- modules/nf-core/custom/catadditionalfasta/environment.yml | 2 +- modules/nf-core/custom/getchromsizes/environment.yml | 2 +- modules/nf-core/custom/tx2gene/environment.yml | 2 +- modules/nf-core/dupradar/environment.yml | 2 +- modules/nf-core/fastp/environment.yml | 2 +- modules/nf-core/fastqc/environment.yml | 2 +- modules/nf-core/fq/subsample/environment.yml | 2 +- modules/nf-core/gffread/environment.yml | 2 +- modules/nf-core/gunzip/environment.yml | 2 +- modules/nf-core/hisat2/align/environment.yml | 4 ++-- modules/nf-core/hisat2/build/environment.yml | 2 +- modules/nf-core/hisat2/extractsplicesites/environment.yml | 2 +- modules/nf-core/kallisto/index/environment.yml | 2 +- modules/nf-core/kallisto/quant/environment.yml | 2 +- modules/nf-core/multiqc/environment.yml | 2 +- modules/nf-core/picard/markduplicates/environment.yml | 2 +- modules/nf-core/preseq/lcextrap/environment.yml | 2 +- modules/nf-core/qualimap/rnaseq/environment.yml | 2 +- modules/nf-core/rsem/calculateexpression/environment.yml | 5 +++-- modules/nf-core/rsem/preparereference/environment.yml | 5 +++-- modules/nf-core/rseqc/bamstat/environment.yml | 4 ++-- modules/nf-core/rseqc/inferexperiment/environment.yml | 4 ++-- modules/nf-core/rseqc/innerdistance/environment.yml | 4 ++-- modules/nf-core/rseqc/junctionannotation/environment.yml | 4 ++-- modules/nf-core/rseqc/junctionsaturation/environment.yml | 4 ++-- modules/nf-core/rseqc/readdistribution/environment.yml | 4 ++-- modules/nf-core/rseqc/readduplication/environment.yml | 4 ++-- modules/nf-core/rseqc/tin/environment.yml | 4 ++-- modules/nf-core/salmon/index/environment.yml | 2 +- modules/nf-core/salmon/quant/environment.yml | 2 +- modules/nf-core/samtools/flagstat/environment.yml | 4 ++-- modules/nf-core/samtools/idxstats/environment.yml | 4 ++-- modules/nf-core/samtools/index/environment.yml | 4 ++-- modules/nf-core/samtools/sort/environment.yml | 4 ++-- modules/nf-core/samtools/sort/main.nf | 1 - modules/nf-core/samtools/stats/environment.yml | 4 ++-- modules/nf-core/sortmerna/environment.yml | 2 +- modules/nf-core/star/align/environment.yml | 8 ++++---- modules/nf-core/star/genomegenerate/environment.yml | 8 ++++---- modules/nf-core/stringtie/stringtie/environment.yml | 2 +- modules/nf-core/subread/featurecounts/environment.yml | 2 +- .../summarizedexperiment/environment.yml | 2 +- modules/nf-core/trimgalore/environment.yml | 4 ++-- modules/nf-core/tximeta/tximport/environment.yml | 2 +- modules/nf-core/ucsc/bedclip/environment.yml | 2 +- modules/nf-core/ucsc/bedgraphtobigwig/environment.yml | 2 +- modules/nf-core/umitools/dedup/environment.yml | 2 +- modules/nf-core/umitools/extract/environment.yml | 2 +- modules/nf-core/umitools/prepareforrsem/environment.yml | 2 +- modules/nf-core/untar/environment.yml | 6 +++--- nextflow.config | 2 +- workflows/rnaseq/main.nf | 2 +- 58 files changed, 85 insertions(+), 83 deletions(-) diff --git a/modules/local/star_align_igenomes/main.nf b/modules/local/star_align_igenomes/main.nf index 32f3cac29..22981ed06 100644 --- a/modules/local/star_align_igenomes/main.nf +++ b/modules/local/star_align_igenomes/main.nf @@ -2,7 +2,7 @@ process STAR_ALIGN_IGENOMES { tag "$meta.id" label 'process_high' - conda "bioconda::star=2.6.1d bioconda::samtools=1.10 conda-forge::gawk=5.1.0" + conda "seqera::star=2.6.1d bioconda::samtools conda-forge::gawk=5.1.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0' : 'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0' }" diff --git a/modules/local/star_genomegenerate_igenomes/main.nf b/modules/local/star_genomegenerate_igenomes/main.nf index 814bc7c8c..c36025b05 100644 --- a/modules/local/star_genomegenerate_igenomes/main.nf +++ b/modules/local/star_genomegenerate_igenomes/main.nf @@ -2,7 +2,7 @@ process STAR_GENOMEGENERATE_IGENOMES { tag "$fasta" label 'process_high' - conda "bioconda::star=2.6.1d bioconda::samtools=1.10 conda-forge::gawk=5.1.0" + conda "bioconda::star bioconda::samtools conda-forge::gawk=5.1.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0' : 'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0' }" diff --git a/modules/nf-core/bbmap/bbsplit/environment.yml b/modules/nf-core/bbmap/bbsplit/environment.yml index 4c6db6276..2e7bb8194 100644 --- a/modules/nf-core/bbmap/bbsplit/environment.yml +++ b/modules/nf-core/bbmap/bbsplit/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::bbmap=39.01 + - bioconda::bbmap diff --git a/modules/nf-core/bedtools/genomecov/environment.yml b/modules/nf-core/bedtools/genomecov/environment.yml index 8fbe20c31..4d4e55eaf 100644 --- a/modules/nf-core/bedtools/genomecov/environment.yml +++ b/modules/nf-core/bedtools/genomecov/environment.yml @@ -1,7 +1,8 @@ name: bedtools_genomecov channels: + - seqera - conda-forge - bioconda - defaults dependencies: - - bioconda::bedtools=2.31.1 + - bioconda::bedtools diff --git a/modules/nf-core/bedtools/genomecov/main.nf b/modules/nf-core/bedtools/genomecov/main.nf index 954e8913d..b02bf1cfe 100644 --- a/modules/nf-core/bedtools/genomecov/main.nf +++ b/modules/nf-core/bedtools/genomecov/main.nf @@ -27,7 +27,7 @@ process BEDTOOLS_GENOMECOV { if (!args_list.contains('-bg') && (scale > 0 && scale != 1)) { args += " -bg" } - def sort_cmd = sort ? '| bedtools sort' : '' + def sort_cmd = sort ? '| sort -k1,1 -k2,2n' : '' def prefix = task.ext.prefix ?: "${meta.id}" if (intervals.name =~ /\.bam/) { diff --git a/modules/nf-core/cat/fastq/environment.yml b/modules/nf-core/cat/fastq/environment.yml index 8c69b121f..7a9bebebf 100644 --- a/modules/nf-core/cat/fastq/environment.yml +++ b/modules/nf-core/cat/fastq/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - conda-forge::coreutils=8.30 + - conda-forge::coreutils diff --git a/modules/nf-core/custom/catadditionalfasta/environment.yml b/modules/nf-core/custom/catadditionalfasta/environment.yml index 5e757bf4c..a801ae936 100644 --- a/modules/nf-core/custom/catadditionalfasta/environment.yml +++ b/modules/nf-core/custom/catadditionalfasta/environment.yml @@ -6,4 +6,4 @@ channels: - bioconda - defaults dependencies: - - conda-forge::python=3.9.5" + - conda-forge::python" diff --git a/modules/nf-core/custom/getchromsizes/environment.yml b/modules/nf-core/custom/getchromsizes/environment.yml index 2a01695f1..7555c59ee 100644 --- a/modules/nf-core/custom/getchromsizes/environment.yml +++ b/modules/nf-core/custom/getchromsizes/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::samtools=1.16.1 + - bioconda::samtools diff --git a/modules/nf-core/custom/tx2gene/environment.yml b/modules/nf-core/custom/tx2gene/environment.yml index a859dc881..638bc4a75 100644 --- a/modules/nf-core/custom/tx2gene/environment.yml +++ b/modules/nf-core/custom/tx2gene/environment.yml @@ -6,4 +6,4 @@ channels: - bioconda - defaults dependencies: - - python=3.9.5 + - python diff --git a/modules/nf-core/dupradar/environment.yml b/modules/nf-core/dupradar/environment.yml index 58b2bf11d..0f6aa3d2b 100644 --- a/modules/nf-core/dupradar/environment.yml +++ b/modules/nf-core/dupradar/environment.yml @@ -6,4 +6,4 @@ channels: - bioconda - defaults dependencies: - - "bioconda::bioconductor-dupradar=1.32.0" + - "bioconda::bioconductor-dupradar" diff --git a/modules/nf-core/fastp/environment.yml b/modules/nf-core/fastp/environment.yml index 70389e664..6970ba186 100644 --- a/modules/nf-core/fastp/environment.yml +++ b/modules/nf-core/fastp/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::fastp=0.23.4 + - bioconda::fastp diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml index 1787b38a9..936bf0896 100644 --- a/modules/nf-core/fastqc/environment.yml +++ b/modules/nf-core/fastqc/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::fastqc=0.12.1 + - bioconda::fastqc diff --git a/modules/nf-core/fq/subsample/environment.yml b/modules/nf-core/fq/subsample/environment.yml index c588de38a..71231aa8b 100644 --- a/modules/nf-core/fq/subsample/environment.yml +++ b/modules/nf-core/fq/subsample/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::fq=0.9.1 + - bioconda::fq diff --git a/modules/nf-core/gffread/environment.yml b/modules/nf-core/gffread/environment.yml index 5398f71c5..17e6bb6cb 100644 --- a/modules/nf-core/gffread/environment.yml +++ b/modules/nf-core/gffread/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::gffread=0.12.1 + - bioconda::gffread diff --git a/modules/nf-core/gunzip/environment.yml b/modules/nf-core/gunzip/environment.yml index 25910b340..d05be27a8 100644 --- a/modules/nf-core/gunzip/environment.yml +++ b/modules/nf-core/gunzip/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - conda-forge::sed=4.7 + - conda-forge::sed diff --git a/modules/nf-core/hisat2/align/environment.yml b/modules/nf-core/hisat2/align/environment.yml index 0c1415f94..f10c74a40 100644 --- a/modules/nf-core/hisat2/align/environment.yml +++ b/modules/nf-core/hisat2/align/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::hisat2=2.2.1 - - bioconda::samtools=1.16.1 + - bioconda::hisat2 + - bioconda::samtools diff --git a/modules/nf-core/hisat2/build/environment.yml b/modules/nf-core/hisat2/build/environment.yml index 2e67cd3ea..78fa8b257 100644 --- a/modules/nf-core/hisat2/build/environment.yml +++ b/modules/nf-core/hisat2/build/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::hisat2=2.2.1 + - bioconda::hisat2 diff --git a/modules/nf-core/hisat2/extractsplicesites/environment.yml b/modules/nf-core/hisat2/extractsplicesites/environment.yml index 4b03e5e46..4ae5a0986 100644 --- a/modules/nf-core/hisat2/extractsplicesites/environment.yml +++ b/modules/nf-core/hisat2/extractsplicesites/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::hisat2=2.2.1 + - bioconda::hisat2 diff --git a/modules/nf-core/kallisto/index/environment.yml b/modules/nf-core/kallisto/index/environment.yml index 471b006a8..5ddd1ce3f 100644 --- a/modules/nf-core/kallisto/index/environment.yml +++ b/modules/nf-core/kallisto/index/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::kallisto=0.48.0 + - bioconda::kallisto diff --git a/modules/nf-core/kallisto/quant/environment.yml b/modules/nf-core/kallisto/quant/environment.yml index c2d6306bb..8b95f28f3 100644 --- a/modules/nf-core/kallisto/quant/environment.yml +++ b/modules/nf-core/kallisto/quant/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::kallisto=0.48.0 + - bioconda::kallisto diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index ca39fb67e..7c7e1e5d7 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::multiqc=1.21 + - bioconda::multiqc diff --git a/modules/nf-core/picard/markduplicates/environment.yml b/modules/nf-core/picard/markduplicates/environment.yml index 58b795f54..7e0b0b34c 100644 --- a/modules/nf-core/picard/markduplicates/environment.yml +++ b/modules/nf-core/picard/markduplicates/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::picard=3.1.1 + - bioconda::picard diff --git a/modules/nf-core/preseq/lcextrap/environment.yml b/modules/nf-core/preseq/lcextrap/environment.yml index 57b8b9c67..7d8613bcc 100644 --- a/modules/nf-core/preseq/lcextrap/environment.yml +++ b/modules/nf-core/preseq/lcextrap/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::preseq=3.1.2 + - bioconda::preseq diff --git a/modules/nf-core/qualimap/rnaseq/environment.yml b/modules/nf-core/qualimap/rnaseq/environment.yml index 590ae85f7..f1f0b04db 100644 --- a/modules/nf-core/qualimap/rnaseq/environment.yml +++ b/modules/nf-core/qualimap/rnaseq/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::qualimap=2.3 + - bioconda::qualimap diff --git a/modules/nf-core/rsem/calculateexpression/environment.yml b/modules/nf-core/rsem/calculateexpression/environment.yml index b811fa6fe..47d0158ab 100644 --- a/modules/nf-core/rsem/calculateexpression/environment.yml +++ b/modules/nf-core/rsem/calculateexpression/environment.yml @@ -1,8 +1,9 @@ name: rsem_calculateexpression channels: + - seqera - conda-forge - bioconda - defaults dependencies: - - bioconda::rsem=1.3.3 - - bioconda::star=2.7.10a + - bioconda::rsem + - bioconda::star diff --git a/modules/nf-core/rsem/preparereference/environment.yml b/modules/nf-core/rsem/preparereference/environment.yml index c80e69106..c4ef537cb 100644 --- a/modules/nf-core/rsem/preparereference/environment.yml +++ b/modules/nf-core/rsem/preparereference/environment.yml @@ -1,8 +1,9 @@ name: rsem_preparereference channels: + - seqera - conda-forge - bioconda - defaults dependencies: - - bioconda::rsem=1.3.3 - - bioconda::star=2.7.10a + - seqera::rsem + - seqera::star=2.6.1d diff --git a/modules/nf-core/rseqc/bamstat/environment.yml b/modules/nf-core/rseqc/bamstat/environment.yml index e960c9943..2894094ee 100644 --- a/modules/nf-core/rseqc/bamstat/environment.yml +++ b/modules/nf-core/rseqc/bamstat/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::rseqc=5.0.3 - - conda-forge::r-base>=3.5 + - bioconda::rseqc + - conda-forge::r-base diff --git a/modules/nf-core/rseqc/inferexperiment/environment.yml b/modules/nf-core/rseqc/inferexperiment/environment.yml index 78215985a..e6affc939 100644 --- a/modules/nf-core/rseqc/inferexperiment/environment.yml +++ b/modules/nf-core/rseqc/inferexperiment/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::rseqc=5.0.3 - - conda-forge::r-base>=3.5 + - bioconda::rseqc + - conda-forge::r-base diff --git a/modules/nf-core/rseqc/innerdistance/environment.yml b/modules/nf-core/rseqc/innerdistance/environment.yml index fb6e9e925..bb7838a3f 100644 --- a/modules/nf-core/rseqc/innerdistance/environment.yml +++ b/modules/nf-core/rseqc/innerdistance/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::rseqc=5.0.3 - - conda-forge::r-base>=3.5 + - bioconda::rseqc + - conda-forge::r-base diff --git a/modules/nf-core/rseqc/junctionannotation/environment.yml b/modules/nf-core/rseqc/junctionannotation/environment.yml index 35276b715..9c43c0d5a 100644 --- a/modules/nf-core/rseqc/junctionannotation/environment.yml +++ b/modules/nf-core/rseqc/junctionannotation/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::rseqc=5.0.3 - - conda-forge::r-base>=3.5 + - bioconda::rseqc + - conda-forge::r-base diff --git a/modules/nf-core/rseqc/junctionsaturation/environment.yml b/modules/nf-core/rseqc/junctionsaturation/environment.yml index 7b9cc4fa7..7e2607545 100644 --- a/modules/nf-core/rseqc/junctionsaturation/environment.yml +++ b/modules/nf-core/rseqc/junctionsaturation/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::rseqc=5.0.3 - - conda-forge::r-base>=3.5 + - bioconda::rseqc + - conda-forge::r-base diff --git a/modules/nf-core/rseqc/readdistribution/environment.yml b/modules/nf-core/rseqc/readdistribution/environment.yml index 59be9fa88..dcdc0defd 100644 --- a/modules/nf-core/rseqc/readdistribution/environment.yml +++ b/modules/nf-core/rseqc/readdistribution/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::rseqc=5.0.3 - - conda-forge::r-base>=3.5 + - bioconda::rseqc + - conda-forge::r-base diff --git a/modules/nf-core/rseqc/readduplication/environment.yml b/modules/nf-core/rseqc/readduplication/environment.yml index c99f107a1..3600c7054 100644 --- a/modules/nf-core/rseqc/readduplication/environment.yml +++ b/modules/nf-core/rseqc/readduplication/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::rseqc=5.0.3 - - conda-forge::r-base>=3.5 + - bioconda::rseqc + - conda-forge::r-base diff --git a/modules/nf-core/rseqc/tin/environment.yml b/modules/nf-core/rseqc/tin/environment.yml index 288da4300..f24194b5f 100644 --- a/modules/nf-core/rseqc/tin/environment.yml +++ b/modules/nf-core/rseqc/tin/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::rseqc=5.0.3 - - conda-forge::r-base>=3.5 + - bioconda::rseqc + - conda-forge::r-base diff --git a/modules/nf-core/salmon/index/environment.yml b/modules/nf-core/salmon/index/environment.yml index a6607d964..29f762517 100644 --- a/modules/nf-core/salmon/index/environment.yml +++ b/modules/nf-core/salmon/index/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::salmon=1.10.1 + - bioconda::salmon diff --git a/modules/nf-core/salmon/quant/environment.yml b/modules/nf-core/salmon/quant/environment.yml index 862667241..28439bdbe 100644 --- a/modules/nf-core/salmon/quant/environment.yml +++ b/modules/nf-core/salmon/quant/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::salmon=1.10.1 + - bioconda::salmon diff --git a/modules/nf-core/samtools/flagstat/environment.yml b/modules/nf-core/samtools/flagstat/environment.yml index bd57cb54d..cd58f431d 100644 --- a/modules/nf-core/samtools/flagstat/environment.yml +++ b/modules/nf-core/samtools/flagstat/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::samtools=1.19.2 - - bioconda::htslib=1.19.1 + - bioconda::samtools + - bioconda::htslib diff --git a/modules/nf-core/samtools/idxstats/environment.yml b/modules/nf-core/samtools/idxstats/environment.yml index 174973b88..5d0378237 100644 --- a/modules/nf-core/samtools/idxstats/environment.yml +++ b/modules/nf-core/samtools/idxstats/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::samtools=1.19.2 - - bioconda::htslib=1.19.1 + - bioconda::samtools + - bioconda::htslib diff --git a/modules/nf-core/samtools/index/environment.yml b/modules/nf-core/samtools/index/environment.yml index a5e506498..84b752bde 100644 --- a/modules/nf-core/samtools/index/environment.yml +++ b/modules/nf-core/samtools/index/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::samtools=1.19.2 - - bioconda::htslib=1.19.1 + - bioconda::samtools + - bioconda::htslib diff --git a/modules/nf-core/samtools/sort/environment.yml b/modules/nf-core/samtools/sort/environment.yml index 4d898e486..fbb6233ea 100644 --- a/modules/nf-core/samtools/sort/environment.yml +++ b/modules/nf-core/samtools/sort/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::samtools=1.19.2 - - bioconda::htslib=1.19.1 + - bioconda::samtools + - bioconda::htslib diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf index fc374f980..0aed6b796 100644 --- a/modules/nf-core/samtools/sort/main.nf +++ b/modules/nf-core/samtools/sort/main.nf @@ -32,7 +32,6 @@ process SAMTOOLS_SORT { """ samtools cat \\ - --threads $task.cpus \\ ${bam} \\ | \\ samtools sort \\ diff --git a/modules/nf-core/samtools/stats/environment.yml b/modules/nf-core/samtools/stats/environment.yml index 67bb0ca40..74f55132b 100644 --- a/modules/nf-core/samtools/stats/environment.yml +++ b/modules/nf-core/samtools/stats/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::samtools=1.19.2 - - bioconda::htslib=1.19.1 + - bioconda::samtools + - bioconda::htslib diff --git a/modules/nf-core/sortmerna/environment.yml b/modules/nf-core/sortmerna/environment.yml index f40f9958d..369a72994 100644 --- a/modules/nf-core/sortmerna/environment.yml +++ b/modules/nf-core/sortmerna/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::sortmerna=4.3.6 + - bioconda::sortmerna diff --git a/modules/nf-core/star/align/environment.yml b/modules/nf-core/star/align/environment.yml index 8bd58cff5..f639ccfb0 100644 --- a/modules/nf-core/star/align/environment.yml +++ b/modules/nf-core/star/align/environment.yml @@ -4,7 +4,7 @@ channels: - bioconda - defaults dependencies: - - bioconda::star=2.7.10a - - bioconda::samtools=1.18 - - bioconda::htslib=1.18 - - conda-forge::gawk=5.1.0 + - bioconda::star + - bioconda::samtools + - bioconda::htslib + - conda-forge::gawk diff --git a/modules/nf-core/star/genomegenerate/environment.yml b/modules/nf-core/star/genomegenerate/environment.yml index 791f255e5..1170105b5 100644 --- a/modules/nf-core/star/genomegenerate/environment.yml +++ b/modules/nf-core/star/genomegenerate/environment.yml @@ -4,7 +4,7 @@ channels: - bioconda - defaults dependencies: - - bioconda::samtools=1.18 - - bioconda::htslib=1.18 - - bioconda::star=2.7.10a - - conda-forge::gawk=5.1.0 + - bioconda::samtools + - bioconda::htslib + - bioconda::star + - conda-forge::gawk diff --git a/modules/nf-core/stringtie/stringtie/environment.yml b/modules/nf-core/stringtie/stringtie/environment.yml index 7a0eccdb8..7c3a0158d 100644 --- a/modules/nf-core/stringtie/stringtie/environment.yml +++ b/modules/nf-core/stringtie/stringtie/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::stringtie=2.2.1 + - bioconda::stringtie diff --git a/modules/nf-core/subread/featurecounts/environment.yml b/modules/nf-core/subread/featurecounts/environment.yml index ca19439d7..812744486 100644 --- a/modules/nf-core/subread/featurecounts/environment.yml +++ b/modules/nf-core/subread/featurecounts/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::subread=2.0.1 + - bioconda::subread diff --git a/modules/nf-core/summarizedexperiment/summarizedexperiment/environment.yml b/modules/nf-core/summarizedexperiment/summarizedexperiment/environment.yml index 252ace791..f97e7d943 100644 --- a/modules/nf-core/summarizedexperiment/summarizedexperiment/environment.yml +++ b/modules/nf-core/summarizedexperiment/summarizedexperiment/environment.yml @@ -6,4 +6,4 @@ channels: - bioconda - defaults dependencies: - - "bioconda::bioconductor-summarizedexperiment=1.32.0" + - "bioconda::bioconductor-summarizedexperiment" diff --git a/modules/nf-core/trimgalore/environment.yml b/modules/nf-core/trimgalore/environment.yml index 17b39f4a5..234bca959 100644 --- a/modules/nf-core/trimgalore/environment.yml +++ b/modules/nf-core/trimgalore/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::trim-galore=0.6.7 - - bioconda::cutadapt=3.4 + - bioconda::trim-galore + - bioconda::cutadapt diff --git a/modules/nf-core/tximeta/tximport/environment.yml b/modules/nf-core/tximeta/tximport/environment.yml index 24b202222..4649d1759 100644 --- a/modules/nf-core/tximeta/tximport/environment.yml +++ b/modules/nf-core/tximeta/tximport/environment.yml @@ -6,4 +6,4 @@ channels: - bioconda - defaults dependencies: - - "bioconda::bioconductor-tximeta=1.20.1" + - "bioconda::bioconductor-tximeta" diff --git a/modules/nf-core/ucsc/bedclip/environment.yml b/modules/nf-core/ucsc/bedclip/environment.yml index 571dc2749..ae7bcb0d1 100644 --- a/modules/nf-core/ucsc/bedclip/environment.yml +++ b/modules/nf-core/ucsc/bedclip/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::ucsc-bedclip=377 + - bioconda::ucsc-bedclip diff --git a/modules/nf-core/ucsc/bedgraphtobigwig/environment.yml b/modules/nf-core/ucsc/bedgraphtobigwig/environment.yml index f91e216f5..1e6658778 100644 --- a/modules/nf-core/ucsc/bedgraphtobigwig/environment.yml +++ b/modules/nf-core/ucsc/bedgraphtobigwig/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::ucsc-bedgraphtobigwig=445 + - bioconda::ucsc-bedgraphtobigwig diff --git a/modules/nf-core/umitools/dedup/environment.yml b/modules/nf-core/umitools/dedup/environment.yml index bc497824f..173040160 100644 --- a/modules/nf-core/umitools/dedup/environment.yml +++ b/modules/nf-core/umitools/dedup/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::umi_tools=1.1.5 + - bioconda::umi_tools diff --git a/modules/nf-core/umitools/extract/environment.yml b/modules/nf-core/umitools/extract/environment.yml index aab452d1e..0d979b32c 100644 --- a/modules/nf-core/umitools/extract/environment.yml +++ b/modules/nf-core/umitools/extract/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::umi_tools=1.1.5 + - bioconda::umi_tools diff --git a/modules/nf-core/umitools/prepareforrsem/environment.yml b/modules/nf-core/umitools/prepareforrsem/environment.yml index dbb1bde77..cf83ff218 100644 --- a/modules/nf-core/umitools/prepareforrsem/environment.yml +++ b/modules/nf-core/umitools/prepareforrsem/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::umi_tools=1.1.5 + - bioconda::umi_tools diff --git a/modules/nf-core/untar/environment.yml b/modules/nf-core/untar/environment.yml index 0c9cbb101..fbf281f50 100644 --- a/modules/nf-core/untar/environment.yml +++ b/modules/nf-core/untar/environment.yml @@ -6,6 +6,6 @@ channels: - defaults dependencies: - - conda-forge::grep=3.11 - - conda-forge::sed=4.7 - - conda-forge::tar=1.34 + - conda-forge::grep + - conda-forge::sed + - conda-forge::tar diff --git a/nextflow.config b/nextflow.config index ca0d3a7e6..1164e2542 100644 --- a/nextflow.config +++ b/nextflow.config @@ -123,7 +123,7 @@ params { // Max resource options // Defaults only, expecting to be overwritten - max_memory = '128.GB' + max_memory = '256.GB' max_cpus = 16 max_time = '240.h' diff --git a/workflows/rnaseq/main.nf b/workflows/rnaseq/main.nf index b679a4b34..13c5bf118 100755 --- a/workflows/rnaseq/main.nf +++ b/workflows/rnaseq/main.nf @@ -142,7 +142,7 @@ workflow RNASEQ { .reads .mix(ch_fastq.single) .set { ch_cat_fastq } - ch_versions = ch_versions.mix(CAT_FASTQ.out.versions.first().ifEmpty(null)) + ch_versions = ch_versions.mix(CAT_FASTQ.out.versions.first()) // // SUBWORKFLOW: Read QC, extract UMI and trim adapters with TrimGalore! From 4bdae48230c5b1bc9f8c0cdbdecce342f8ecb4cf Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Thu, 17 Oct 2024 12:50:30 +0100 Subject: [PATCH 02/18] Fix up config --- conf/arm.config | 146 ++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 146 insertions(+) create mode 100644 conf/arm.config diff --git a/conf/arm.config b/conf/arm.config new file mode 100644 index 000000000..345e38efd --- /dev/null +++ b/conf/arm.config @@ -0,0 +1,146 @@ +// Apply software overrides for ARM compatibility + +withName: '.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' { + conda = 'seqera::star=2.6.1d bioconda::samtools conda-forge::gawk=5.1.0' +} + +withName: 'STAR_GENOMEGENERATE_IGENOMES' { + conda = 'bioconda::star bioconda::samtools conda-forge::gawk=5.1.0' +} + +withName: 'BBSPLIT' { + conda = 'bioconda::bbmap' +} + +withName: 'BEDTOOLS_GENOMECOV' { + conda = 'bioconda::bedtools' +} + +withName: 'CAT_FASTQ' { + conda = 'conda-forge::coreutils' +} + +withName: 'CAT_ADDITIONAL_FASTA' { + conda = 'conda-forge::python' +} + +withName: 'CUSTOM_GETCHROMSIZES' { + conda = 'bioconda::samtools' +} + +withName: 'CUSTOM_TX2GENE' { + conda = 'python' +} + +withName: 'DUPRADAR' { + conda = 'bioconda::bioconductor-dupradar' +} + +withName: 'FASTP' { + conda = 'bioconda::fastp' +} + +withName: 'FQ_SUBSAMPLE' { + conda = 'bioconda::fq' +} + +withName: 'GFFREAD' { + conda = 'bioconda::gffread' +} + +withName: 'GUNZIP' { + conda = 'conda-forge::sed' +} + +withName: 'HISAT2_ALIGN' { + conda = 'bioconda::hisat2 bioconda::samtools' +} + +withName: 'HISAT2_BUILD|HISAT2_EXTRACTSPLICESITES' { + conda = 'bioconda::hisat2' +} + +withName: 'KALLISTO_INDEX|KALLISTO_QUANT' { + conda = 'bioconda::kallisto' +} + +withName: 'MULTIQC' { + conda = 'bioconda::multiqc' +} + +withName: 'PICARD_MARKDUPLICATES' { + conda = 'bioconda::picard' +} + +withName: 'PRESEQ_LCEXTRAP' { + conda = 'bioconda::preseq' +} + +withName: 'QUALIMAP_RNASEQ' { + conda = 'bioconda::qualimap' +} + +withName: 'RSEM_CALCULATEEXPRESSION' { + conda = 'bioconda::rsem bioconda::star' +} + +withName: 'RSEM_PREPAREREFERENCE' { + conda = 'seqera::rsem seqera::star=2.6.1d' +} + +withName: 'RSEQC_BAMSTAT|RSEQC_INFEREXPERIMENT|RSEQC_INNERDISTANCE|RSEQC_JUNCTIONANNOTATION|RSEQC_JUNCTIONSATURATION|RSEQC_READDISTRIBUTION|RSEQC_READDUPLICATION|RSEQC_TIN' { + conda = 'bioconda::rseqc conda-forge::r-base' +} + +withName: 'SALMON_INDEX|SALMON_QUANT' { + conda = 'bioconda::salmon' +} + +withName: 'SAMTOOLS_FLAGSTAT|SAMTOOLS_IDXSTATS|SAMTOOLS_INDEX|SAMTOOLS_SORT|SAMTOOLS_STATS' { + conda = 'bioconda::samtools bioconda::htslib' +} + +withName: 'SORTMERNA' { + conda = 'bioconda::sortmerna' +} + +withName: 'STAR_ALIGN|STAR_GENOMEGENERATE' { + conda = 'bioconda::star bioconda::samtools bioconda::htslib conda-forge::gawk' +} + +withName: 'STRINGTIE_STRINGTIE' { + conda = 'bioconda::stringtie' +} + +withName: 'SUBREAD_FEATURECOUNTS' { + conda = 'bioconda::subread' +} + +withName: 'SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT' { + conda = 'bioconda::bioconductor-summarizedexperiment' +} + +withName: 'TXIMETA_TXIMPORT' { + conda = 'bioconda::bioconductor-tximeta' +} + +withName: 'TRIMGALORE' { + conda = 'bioconda::trim-galore bioconda::cutadapt' +} + +withName: 'UCSC_BEDCLIP' { + conda = 'bioconda::ucsc-bedclip' +} + +withName: 'UCSC_BEDGRAPHTOBIGWIG' { + conda = 'bioconda::ucsc-bedgraphtobigwig' +} + +withName: 'UMITOOLS_DEDUP|UMITOOLS_EXTRACT|UMITOOLS_PREPAREFORRSEM' { + conda = 'bioconda::umi_tools' +} + +withName: 'UNTAR' { + conda = 'conda-forge::grep conda-forge::sed conda-forge::tar' +} + From c9d616ba7c72eb0eae9ebeec5c44eaa9cd6529d2 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Thu, 17 Oct 2024 12:52:30 +0100 Subject: [PATCH 03/18] Reset environment ymls --- modules/nf-core/bbmap/bbsplit/environment.yml | 2 +- modules/nf-core/bedtools/genomecov/environment.yml | 3 +-- modules/nf-core/cat/fastq/environment.yml | 2 +- modules/nf-core/custom/catadditionalfasta/environment.yml | 2 +- modules/nf-core/custom/getchromsizes/environment.yml | 3 ++- modules/nf-core/custom/tx2gene/environment.yml | 2 +- modules/nf-core/dupradar/environment.yml | 2 +- modules/nf-core/fastp/environment.yml | 2 +- modules/nf-core/fastqc/environment.yml | 2 +- modules/nf-core/fq/subsample/environment.yml | 2 +- modules/nf-core/gffread/environment.yml | 2 +- modules/nf-core/gunzip/environment.yml | 4 +++- modules/nf-core/hisat2/align/environment.yml | 4 ++-- modules/nf-core/hisat2/build/environment.yml | 2 +- modules/nf-core/hisat2/extractsplicesites/environment.yml | 2 +- modules/nf-core/kallisto/index/environment.yml | 2 +- modules/nf-core/kallisto/quant/environment.yml | 2 +- modules/nf-core/multiqc/environment.yml | 2 +- modules/nf-core/picard/markduplicates/environment.yml | 2 +- modules/nf-core/preseq/lcextrap/environment.yml | 2 +- modules/nf-core/qualimap/rnaseq/environment.yml | 2 +- modules/nf-core/rsem/calculateexpression/environment.yml | 5 ++--- modules/nf-core/rsem/preparereference/environment.yml | 5 ++--- modules/nf-core/rseqc/bamstat/environment.yml | 4 ++-- modules/nf-core/rseqc/inferexperiment/environment.yml | 4 ++-- modules/nf-core/rseqc/innerdistance/environment.yml | 4 ++-- modules/nf-core/rseqc/junctionannotation/environment.yml | 4 ++-- modules/nf-core/rseqc/junctionsaturation/environment.yml | 4 ++-- modules/nf-core/rseqc/readdistribution/environment.yml | 4 ++-- modules/nf-core/rseqc/readduplication/environment.yml | 4 ++-- modules/nf-core/rseqc/tin/environment.yml | 4 ++-- modules/nf-core/salmon/index/environment.yml | 2 +- modules/nf-core/salmon/quant/environment.yml | 2 +- modules/nf-core/samtools/flagstat/environment.yml | 4 ++-- modules/nf-core/samtools/idxstats/environment.yml | 4 ++-- modules/nf-core/samtools/index/environment.yml | 4 ++-- modules/nf-core/samtools/sort/environment.yml | 4 ++-- modules/nf-core/samtools/stats/environment.yml | 4 ++-- modules/nf-core/sortmerna/environment.yml | 2 +- modules/nf-core/star/align/environment.yml | 8 ++++---- modules/nf-core/star/genomegenerate/environment.yml | 8 ++++---- modules/nf-core/stringtie/stringtie/environment.yml | 2 +- modules/nf-core/subread/featurecounts/environment.yml | 2 +- .../summarizedexperiment/environment.yml | 2 +- modules/nf-core/trimgalore/environment.yml | 4 ++-- modules/nf-core/tximeta/tximport/environment.yml | 2 +- modules/nf-core/ucsc/bedclip/environment.yml | 2 +- modules/nf-core/ucsc/bedgraphtobigwig/environment.yml | 2 +- modules/nf-core/umitools/dedup/environment.yml | 2 +- modules/nf-core/umitools/extract/environment.yml | 2 +- modules/nf-core/umitools/prepareforrsem/environment.yml | 2 +- modules/nf-core/untar/environment.yml | 6 +++--- 52 files changed, 80 insertions(+), 80 deletions(-) diff --git a/modules/nf-core/bbmap/bbsplit/environment.yml b/modules/nf-core/bbmap/bbsplit/environment.yml index 3a0ecdf34..dfd8936e1 100644 --- a/modules/nf-core/bbmap/bbsplit/environment.yml +++ b/modules/nf-core/bbmap/bbsplit/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::bbmap + - bioconda::bbmap=39.01 diff --git a/modules/nf-core/bedtools/genomecov/environment.yml b/modules/nf-core/bedtools/genomecov/environment.yml index d415ae6ec..5683bc05f 100644 --- a/modules/nf-core/bedtools/genomecov/environment.yml +++ b/modules/nf-core/bedtools/genomecov/environment.yml @@ -1,6 +1,5 @@ channels: - - seqera - conda-forge - bioconda dependencies: - - bioconda::bedtools + - bioconda::bedtools=2.31.1 diff --git a/modules/nf-core/cat/fastq/environment.yml b/modules/nf-core/cat/fastq/environment.yml index d15cbda27..c7eb9bd1c 100644 --- a/modules/nf-core/cat/fastq/environment.yml +++ b/modules/nf-core/cat/fastq/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - conda-forge::coreutils + - conda-forge::coreutils=8.30 diff --git a/modules/nf-core/custom/catadditionalfasta/environment.yml b/modules/nf-core/custom/catadditionalfasta/environment.yml index fd1010315..1d80d11a9 100644 --- a/modules/nf-core/custom/catadditionalfasta/environment.yml +++ b/modules/nf-core/custom/catadditionalfasta/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - conda-forge::python" \ No newline at end of file + - conda-forge::python=3.9.5 diff --git a/modules/nf-core/custom/getchromsizes/environment.yml b/modules/nf-core/custom/getchromsizes/environment.yml index 96b17c413..da2df5e43 100644 --- a/modules/nf-core/custom/getchromsizes/environment.yml +++ b/modules/nf-core/custom/getchromsizes/environment.yml @@ -2,4 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools \ No newline at end of file + - bioconda::samtools=1.20 + - bioconda::htslib=1.20 diff --git a/modules/nf-core/custom/tx2gene/environment.yml b/modules/nf-core/custom/tx2gene/environment.yml index f626c1c72..9f5f9fb9b 100644 --- a/modules/nf-core/custom/tx2gene/environment.yml +++ b/modules/nf-core/custom/tx2gene/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - python + - python=3.9.5 diff --git a/modules/nf-core/dupradar/environment.yml b/modules/nf-core/dupradar/environment.yml index ca8f5abef..fb16938d2 100644 --- a/modules/nf-core/dupradar/environment.yml +++ b/modules/nf-core/dupradar/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::bioconductor-dupradar" + - "bioconda::bioconductor-dupradar=1.32.0" diff --git a/modules/nf-core/fastp/environment.yml b/modules/nf-core/fastp/environment.yml index de3512e0a..26d4aca5d 100644 --- a/modules/nf-core/fastp/environment.yml +++ b/modules/nf-core/fastp/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::fastp + - bioconda::fastp=0.23.4 diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml index 30e0b77e3..691d4c763 100644 --- a/modules/nf-core/fastqc/environment.yml +++ b/modules/nf-core/fastqc/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::fastqc + - bioconda::fastqc=0.12.1 diff --git a/modules/nf-core/fq/subsample/environment.yml b/modules/nf-core/fq/subsample/environment.yml index f28625955..eaba9339b 100644 --- a/modules/nf-core/fq/subsample/environment.yml +++ b/modules/nf-core/fq/subsample/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::fq + - bioconda::fq=0.9.1 diff --git a/modules/nf-core/gffread/environment.yml b/modules/nf-core/gffread/environment.yml index 61b39921a..ee2398416 100644 --- a/modules/nf-core/gffread/environment.yml +++ b/modules/nf-core/gffread/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gffread \ No newline at end of file + - bioconda::gffread=0.12.7 diff --git a/modules/nf-core/gunzip/environment.yml b/modules/nf-core/gunzip/environment.yml index 86c0feb98..c7794856d 100644 --- a/modules/nf-core/gunzip/environment.yml +++ b/modules/nf-core/gunzip/environment.yml @@ -2,4 +2,6 @@ channels: - conda-forge - bioconda dependencies: - - conda-forge::sed \ No newline at end of file + - conda-forge::grep=3.11 + - conda-forge::sed=4.8 + - conda-forge::tar=1.34 diff --git a/modules/nf-core/hisat2/align/environment.yml b/modules/nf-core/hisat2/align/environment.yml index 75a1d7505..26c62a3bf 100644 --- a/modules/nf-core/hisat2/align/environment.yml +++ b/modules/nf-core/hisat2/align/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::hisat2 - - bioconda::samtools + - bioconda::hisat2=2.2.1 + - bioconda::samtools=1.16.1 diff --git a/modules/nf-core/hisat2/build/environment.yml b/modules/nf-core/hisat2/build/environment.yml index c2696c30e..afced7338 100644 --- a/modules/nf-core/hisat2/build/environment.yml +++ b/modules/nf-core/hisat2/build/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::hisat2 + - bioconda::hisat2=2.2.1 diff --git a/modules/nf-core/hisat2/extractsplicesites/environment.yml b/modules/nf-core/hisat2/extractsplicesites/environment.yml index c2696c30e..afced7338 100644 --- a/modules/nf-core/hisat2/extractsplicesites/environment.yml +++ b/modules/nf-core/hisat2/extractsplicesites/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::hisat2 + - bioconda::hisat2=2.2.1 diff --git a/modules/nf-core/kallisto/index/environment.yml b/modules/nf-core/kallisto/index/environment.yml index 6ccef310c..27be64918 100644 --- a/modules/nf-core/kallisto/index/environment.yml +++ b/modules/nf-core/kallisto/index/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::kallisto + - bioconda::kallisto=0.48.0 diff --git a/modules/nf-core/kallisto/quant/environment.yml b/modules/nf-core/kallisto/quant/environment.yml index 6ccef310c..27be64918 100644 --- a/modules/nf-core/kallisto/quant/environment.yml +++ b/modules/nf-core/kallisto/quant/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::kallisto + - bioconda::kallisto=0.48.0 diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index 103b4c045..6f5b867b7 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::multiqc \ No newline at end of file + - bioconda::multiqc=1.25.1 diff --git a/modules/nf-core/picard/markduplicates/environment.yml b/modules/nf-core/picard/markduplicates/environment.yml index 4dc4357d0..5f919a9a9 100644 --- a/modules/nf-core/picard/markduplicates/environment.yml +++ b/modules/nf-core/picard/markduplicates/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::picard + - bioconda::picard=3.1.1 diff --git a/modules/nf-core/preseq/lcextrap/environment.yml b/modules/nf-core/preseq/lcextrap/environment.yml index 06bec39d0..926d7aece 100644 --- a/modules/nf-core/preseq/lcextrap/environment.yml +++ b/modules/nf-core/preseq/lcextrap/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::preseq + - bioconda::preseq=3.1.2 diff --git a/modules/nf-core/qualimap/rnaseq/environment.yml b/modules/nf-core/qualimap/rnaseq/environment.yml index 28bab2f99..4fa5f4e8e 100644 --- a/modules/nf-core/qualimap/rnaseq/environment.yml +++ b/modules/nf-core/qualimap/rnaseq/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::qualimap + - bioconda::qualimap=2.3 diff --git a/modules/nf-core/rsem/calculateexpression/environment.yml b/modules/nf-core/rsem/calculateexpression/environment.yml index b29ff989b..bcf70fa9a 100644 --- a/modules/nf-core/rsem/calculateexpression/environment.yml +++ b/modules/nf-core/rsem/calculateexpression/environment.yml @@ -1,7 +1,6 @@ channels: - - seqera - conda-forge - bioconda dependencies: - - bioconda::rsem - - bioconda::star + - bioconda::rsem=1.3.3 + - bioconda::star=2.7.10a diff --git a/modules/nf-core/rsem/preparereference/environment.yml b/modules/nf-core/rsem/preparereference/environment.yml index b70d9f18d..bcf70fa9a 100644 --- a/modules/nf-core/rsem/preparereference/environment.yml +++ b/modules/nf-core/rsem/preparereference/environment.yml @@ -1,7 +1,6 @@ channels: - - seqera - conda-forge - bioconda dependencies: - - seqera::rsem - - seqera::star=2.6.1d + - bioconda::rsem=1.3.3 + - bioconda::star=2.7.10a diff --git a/modules/nf-core/rseqc/bamstat/environment.yml b/modules/nf-core/rseqc/bamstat/environment.yml index b82581d16..304e38fcf 100644 --- a/modules/nf-core/rseqc/bamstat/environment.yml +++ b/modules/nf-core/rseqc/bamstat/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::rseqc - - conda-forge::r-base + - bioconda::rseqc=5.0.3 + - conda-forge::r-base>=3.5 diff --git a/modules/nf-core/rseqc/inferexperiment/environment.yml b/modules/nf-core/rseqc/inferexperiment/environment.yml index b82581d16..304e38fcf 100644 --- a/modules/nf-core/rseqc/inferexperiment/environment.yml +++ b/modules/nf-core/rseqc/inferexperiment/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::rseqc - - conda-forge::r-base + - bioconda::rseqc=5.0.3 + - conda-forge::r-base>=3.5 diff --git a/modules/nf-core/rseqc/innerdistance/environment.yml b/modules/nf-core/rseqc/innerdistance/environment.yml index b82581d16..304e38fcf 100644 --- a/modules/nf-core/rseqc/innerdistance/environment.yml +++ b/modules/nf-core/rseqc/innerdistance/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::rseqc - - conda-forge::r-base + - bioconda::rseqc=5.0.3 + - conda-forge::r-base>=3.5 diff --git a/modules/nf-core/rseqc/junctionannotation/environment.yml b/modules/nf-core/rseqc/junctionannotation/environment.yml index b82581d16..304e38fcf 100644 --- a/modules/nf-core/rseqc/junctionannotation/environment.yml +++ b/modules/nf-core/rseqc/junctionannotation/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::rseqc - - conda-forge::r-base + - bioconda::rseqc=5.0.3 + - conda-forge::r-base>=3.5 diff --git a/modules/nf-core/rseqc/junctionsaturation/environment.yml b/modules/nf-core/rseqc/junctionsaturation/environment.yml index b82581d16..304e38fcf 100644 --- a/modules/nf-core/rseqc/junctionsaturation/environment.yml +++ b/modules/nf-core/rseqc/junctionsaturation/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::rseqc - - conda-forge::r-base + - bioconda::rseqc=5.0.3 + - conda-forge::r-base>=3.5 diff --git a/modules/nf-core/rseqc/readdistribution/environment.yml b/modules/nf-core/rseqc/readdistribution/environment.yml index b82581d16..304e38fcf 100644 --- a/modules/nf-core/rseqc/readdistribution/environment.yml +++ b/modules/nf-core/rseqc/readdistribution/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::rseqc - - conda-forge::r-base + - bioconda::rseqc=5.0.3 + - conda-forge::r-base>=3.5 diff --git a/modules/nf-core/rseqc/readduplication/environment.yml b/modules/nf-core/rseqc/readduplication/environment.yml index b82581d16..304e38fcf 100644 --- a/modules/nf-core/rseqc/readduplication/environment.yml +++ b/modules/nf-core/rseqc/readduplication/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::rseqc - - conda-forge::r-base + - bioconda::rseqc=5.0.3 + - conda-forge::r-base>=3.5 diff --git a/modules/nf-core/rseqc/tin/environment.yml b/modules/nf-core/rseqc/tin/environment.yml index b82581d16..304e38fcf 100644 --- a/modules/nf-core/rseqc/tin/environment.yml +++ b/modules/nf-core/rseqc/tin/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::rseqc - - conda-forge::r-base + - bioconda::rseqc=5.0.3 + - conda-forge::r-base>=3.5 diff --git a/modules/nf-core/salmon/index/environment.yml b/modules/nf-core/salmon/index/environment.yml index b4e2d89de..471164faa 100644 --- a/modules/nf-core/salmon/index/environment.yml +++ b/modules/nf-core/salmon/index/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::salmon + - bioconda::salmon=1.10.1 diff --git a/modules/nf-core/salmon/quant/environment.yml b/modules/nf-core/salmon/quant/environment.yml index b4e2d89de..471164faa 100644 --- a/modules/nf-core/salmon/quant/environment.yml +++ b/modules/nf-core/salmon/quant/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::salmon + - bioconda::salmon=1.10.1 diff --git a/modules/nf-core/samtools/flagstat/environment.yml b/modules/nf-core/samtools/flagstat/environment.yml index 55c7b199f..da2df5e43 100644 --- a/modules/nf-core/samtools/flagstat/environment.yml +++ b/modules/nf-core/samtools/flagstat/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools - - bioconda::htslib \ No newline at end of file + - bioconda::samtools=1.20 + - bioconda::htslib=1.20 diff --git a/modules/nf-core/samtools/idxstats/environment.yml b/modules/nf-core/samtools/idxstats/environment.yml index 55c7b199f..da2df5e43 100644 --- a/modules/nf-core/samtools/idxstats/environment.yml +++ b/modules/nf-core/samtools/idxstats/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools - - bioconda::htslib \ No newline at end of file + - bioconda::samtools=1.20 + - bioconda::htslib=1.20 diff --git a/modules/nf-core/samtools/index/environment.yml b/modules/nf-core/samtools/index/environment.yml index 55c7b199f..da2df5e43 100644 --- a/modules/nf-core/samtools/index/environment.yml +++ b/modules/nf-core/samtools/index/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools - - bioconda::htslib \ No newline at end of file + - bioconda::samtools=1.20 + - bioconda::htslib=1.20 diff --git a/modules/nf-core/samtools/sort/environment.yml b/modules/nf-core/samtools/sort/environment.yml index 55c7b199f..da2df5e43 100644 --- a/modules/nf-core/samtools/sort/environment.yml +++ b/modules/nf-core/samtools/sort/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools - - bioconda::htslib \ No newline at end of file + - bioconda::samtools=1.20 + - bioconda::htslib=1.20 diff --git a/modules/nf-core/samtools/stats/environment.yml b/modules/nf-core/samtools/stats/environment.yml index 55c7b199f..da2df5e43 100644 --- a/modules/nf-core/samtools/stats/environment.yml +++ b/modules/nf-core/samtools/stats/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools - - bioconda::htslib \ No newline at end of file + - bioconda::samtools=1.20 + - bioconda::htslib=1.20 diff --git a/modules/nf-core/sortmerna/environment.yml b/modules/nf-core/sortmerna/environment.yml index 6fd5e7442..fab44081f 100644 --- a/modules/nf-core/sortmerna/environment.yml +++ b/modules/nf-core/sortmerna/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::sortmerna + - bioconda::sortmerna=4.3.6 diff --git a/modules/nf-core/star/align/environment.yml b/modules/nf-core/star/align/environment.yml index 0084b66ae..e3d1c714d 100644 --- a/modules/nf-core/star/align/environment.yml +++ b/modules/nf-core/star/align/environment.yml @@ -2,7 +2,7 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::star - - bioconda::samtools - - bioconda::htslib - - conda-forge::gawk + - bioconda::star=2.7.10a + - bioconda::samtools=1.18 + - bioconda::htslib=1.18 + - conda-forge::gawk=5.1.0 diff --git a/modules/nf-core/star/genomegenerate/environment.yml b/modules/nf-core/star/genomegenerate/environment.yml index 6617b4720..38611dfa2 100644 --- a/modules/nf-core/star/genomegenerate/environment.yml +++ b/modules/nf-core/star/genomegenerate/environment.yml @@ -2,7 +2,7 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools - - bioconda::htslib - - bioconda::star - - conda-forge::gawk + - bioconda::samtools=1.18 + - bioconda::htslib=1.18 + - bioconda::star=2.7.10a + - conda-forge::gawk=5.1.0 diff --git a/modules/nf-core/stringtie/stringtie/environment.yml b/modules/nf-core/stringtie/stringtie/environment.yml index 25e1a3810..0556de41a 100644 --- a/modules/nf-core/stringtie/stringtie/environment.yml +++ b/modules/nf-core/stringtie/stringtie/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::stringtie + - bioconda::stringtie=2.2.1 diff --git a/modules/nf-core/subread/featurecounts/environment.yml b/modules/nf-core/subread/featurecounts/environment.yml index 43bff6526..7e919aa31 100644 --- a/modules/nf-core/subread/featurecounts/environment.yml +++ b/modules/nf-core/subread/featurecounts/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::subread + - bioconda::subread=2.0.1 diff --git a/modules/nf-core/summarizedexperiment/summarizedexperiment/environment.yml b/modules/nf-core/summarizedexperiment/summarizedexperiment/environment.yml index 24ce1dcde..dc4e6c936 100644 --- a/modules/nf-core/summarizedexperiment/summarizedexperiment/environment.yml +++ b/modules/nf-core/summarizedexperiment/summarizedexperiment/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::bioconductor-summarizedexperiment" + - "bioconda::bioconductor-summarizedexperiment=1.32.0" diff --git a/modules/nf-core/trimgalore/environment.yml b/modules/nf-core/trimgalore/environment.yml index c83091ea1..f172c1b39 100644 --- a/modules/nf-core/trimgalore/environment.yml +++ b/modules/nf-core/trimgalore/environment.yml @@ -3,5 +3,5 @@ channels: - bioconda dependencies: - - bioconda::trim-galore - - bioconda::cutadapt \ No newline at end of file + - bioconda::cutadapt=3.4 + - bioconda::trim-galore=0.6.7 diff --git a/modules/nf-core/tximeta/tximport/environment.yml b/modules/nf-core/tximeta/tximport/environment.yml index 5c5179f35..4b6df0cfe 100644 --- a/modules/nf-core/tximeta/tximport/environment.yml +++ b/modules/nf-core/tximeta/tximport/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::bioconductor-tximeta" + - "bioconda::bioconductor-tximeta=1.20.1" diff --git a/modules/nf-core/ucsc/bedclip/environment.yml b/modules/nf-core/ucsc/bedclip/environment.yml index 8e6772864..94e825f03 100644 --- a/modules/nf-core/ucsc/bedclip/environment.yml +++ b/modules/nf-core/ucsc/bedclip/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::ucsc-bedclip + - bioconda::ucsc-bedclip=377 diff --git a/modules/nf-core/ucsc/bedgraphtobigwig/environment.yml b/modules/nf-core/ucsc/bedgraphtobigwig/environment.yml index 7eca50fcc..a54fb8f16 100644 --- a/modules/nf-core/ucsc/bedgraphtobigwig/environment.yml +++ b/modules/nf-core/ucsc/bedgraphtobigwig/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::ucsc-bedgraphtobigwig + - bioconda::ucsc-bedgraphtobigwig=445 diff --git a/modules/nf-core/umitools/dedup/environment.yml b/modules/nf-core/umitools/dedup/environment.yml index 2d4e5317c..9f9e03c49 100644 --- a/modules/nf-core/umitools/dedup/environment.yml +++ b/modules/nf-core/umitools/dedup/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::umi_tools + - bioconda::umi_tools=1.1.5 diff --git a/modules/nf-core/umitools/extract/environment.yml b/modules/nf-core/umitools/extract/environment.yml index 2d4e5317c..9f9e03c49 100644 --- a/modules/nf-core/umitools/extract/environment.yml +++ b/modules/nf-core/umitools/extract/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::umi_tools + - bioconda::umi_tools=1.1.5 diff --git a/modules/nf-core/umitools/prepareforrsem/environment.yml b/modules/nf-core/umitools/prepareforrsem/environment.yml index 2d4e5317c..9f9e03c49 100644 --- a/modules/nf-core/umitools/prepareforrsem/environment.yml +++ b/modules/nf-core/umitools/prepareforrsem/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::umi_tools + - bioconda::umi_tools=1.1.5 diff --git a/modules/nf-core/untar/environment.yml b/modules/nf-core/untar/environment.yml index 14e237118..c7794856d 100644 --- a/modules/nf-core/untar/environment.yml +++ b/modules/nf-core/untar/environment.yml @@ -2,6 +2,6 @@ channels: - conda-forge - bioconda dependencies: - - conda-forge::grep - - conda-forge::sed - - conda-forge::tar \ No newline at end of file + - conda-forge::grep=3.11 + - conda-forge::sed=4.8 + - conda-forge::tar=1.34 From 9f640ab5a1b517a0bdd6cb43a9eac5a364edbc4b Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Thu, 17 Oct 2024 12:55:16 +0100 Subject: [PATCH 04/18] Reset main.nfs with software changes only --- modules/local/star_align_igenomes/main.nf | 2 +- modules/local/star_genomegenerate_igenomes/main.nf | 2 +- modules/nf-core/bedtools/genomecov/main.nf | 1 - 3 files changed, 2 insertions(+), 3 deletions(-) diff --git a/modules/local/star_align_igenomes/main.nf b/modules/local/star_align_igenomes/main.nf index 7341d5778..7bda3df84 100644 --- a/modules/local/star_align_igenomes/main.nf +++ b/modules/local/star_align_igenomes/main.nf @@ -2,7 +2,7 @@ process STAR_ALIGN_IGENOMES { tag "$meta.id" label 'process_high' - conda "seqera::star=2.6.1d bioconda::samtools conda-forge::gawk=5.1.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0' : 'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0' }" diff --git a/modules/local/star_genomegenerate_igenomes/main.nf b/modules/local/star_genomegenerate_igenomes/main.nf index 775afde95..4e2fcf6bf 100644 --- a/modules/local/star_genomegenerate_igenomes/main.nf +++ b/modules/local/star_genomegenerate_igenomes/main.nf @@ -2,7 +2,7 @@ process STAR_GENOMEGENERATE_IGENOMES { tag "$fasta" label 'process_high' - conda "bioconda::star bioconda::samtools conda-forge::gawk=5.1.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0' : 'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0' }" diff --git a/modules/nf-core/bedtools/genomecov/main.nf b/modules/nf-core/bedtools/genomecov/main.nf index 98cfd4c8e..91869ec23 100644 --- a/modules/nf-core/bedtools/genomecov/main.nf +++ b/modules/nf-core/bedtools/genomecov/main.nf @@ -27,7 +27,6 @@ process BEDTOOLS_GENOMECOV { if (!args_list.contains('-bg') && (scale > 0 && scale != 1)) { args += " -bg" } - // Sorts output file by chromosome and position using additional options for performance and consistency // See https://www.biostars.org/p/66927/ for further details def buffer = task.memory ? "--buffer-size=${task.memory.toGiga().intdiv(2)}G" : '' From 00cff4c8e48a4cd15bd3fdb9ab92c0bfb2ae141e Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Thu, 17 Oct 2024 12:58:29 +0100 Subject: [PATCH 05/18] Link sw configs to arm profile --- nextflow.config | 1 + 1 file changed, 1 insertion(+) diff --git a/nextflow.config b/nextflow.config index 496a9429f..525c6f4e1 100644 --- a/nextflow.config +++ b/nextflow.config @@ -186,6 +186,7 @@ profiles { } arm { docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' + includeConfig 'conf/arm.config' } singularity { singularity.enabled = true From f281e0b13f63fda6b7a984910ff5db8ce665d072 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Thu, 17 Oct 2024 13:13:27 +0100 Subject: [PATCH 06/18] Add process block --- conf/arm.config | 294 ++++++++++++++++++++++++------------------------ 1 file changed, 148 insertions(+), 146 deletions(-) diff --git a/conf/arm.config b/conf/arm.config index 345e38efd..112cb66af 100644 --- a/conf/arm.config +++ b/conf/arm.config @@ -1,146 +1,148 @@ -// Apply software overrides for ARM compatibility - -withName: '.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' { - conda = 'seqera::star=2.6.1d bioconda::samtools conda-forge::gawk=5.1.0' -} - -withName: 'STAR_GENOMEGENERATE_IGENOMES' { - conda = 'bioconda::star bioconda::samtools conda-forge::gawk=5.1.0' -} - -withName: 'BBSPLIT' { - conda = 'bioconda::bbmap' -} - -withName: 'BEDTOOLS_GENOMECOV' { - conda = 'bioconda::bedtools' -} - -withName: 'CAT_FASTQ' { - conda = 'conda-forge::coreutils' -} - -withName: 'CAT_ADDITIONAL_FASTA' { - conda = 'conda-forge::python' -} - -withName: 'CUSTOM_GETCHROMSIZES' { - conda = 'bioconda::samtools' -} - -withName: 'CUSTOM_TX2GENE' { - conda = 'python' -} - -withName: 'DUPRADAR' { - conda = 'bioconda::bioconductor-dupradar' -} - -withName: 'FASTP' { - conda = 'bioconda::fastp' -} - -withName: 'FQ_SUBSAMPLE' { - conda = 'bioconda::fq' -} - -withName: 'GFFREAD' { - conda = 'bioconda::gffread' -} - -withName: 'GUNZIP' { - conda = 'conda-forge::sed' -} - -withName: 'HISAT2_ALIGN' { - conda = 'bioconda::hisat2 bioconda::samtools' -} - -withName: 'HISAT2_BUILD|HISAT2_EXTRACTSPLICESITES' { - conda = 'bioconda::hisat2' -} - -withName: 'KALLISTO_INDEX|KALLISTO_QUANT' { - conda = 'bioconda::kallisto' -} - -withName: 'MULTIQC' { - conda = 'bioconda::multiqc' -} - -withName: 'PICARD_MARKDUPLICATES' { - conda = 'bioconda::picard' -} - -withName: 'PRESEQ_LCEXTRAP' { - conda = 'bioconda::preseq' -} - -withName: 'QUALIMAP_RNASEQ' { - conda = 'bioconda::qualimap' -} - -withName: 'RSEM_CALCULATEEXPRESSION' { - conda = 'bioconda::rsem bioconda::star' -} - -withName: 'RSEM_PREPAREREFERENCE' { - conda = 'seqera::rsem seqera::star=2.6.1d' -} - -withName: 'RSEQC_BAMSTAT|RSEQC_INFEREXPERIMENT|RSEQC_INNERDISTANCE|RSEQC_JUNCTIONANNOTATION|RSEQC_JUNCTIONSATURATION|RSEQC_READDISTRIBUTION|RSEQC_READDUPLICATION|RSEQC_TIN' { - conda = 'bioconda::rseqc conda-forge::r-base' -} - -withName: 'SALMON_INDEX|SALMON_QUANT' { - conda = 'bioconda::salmon' -} - -withName: 'SAMTOOLS_FLAGSTAT|SAMTOOLS_IDXSTATS|SAMTOOLS_INDEX|SAMTOOLS_SORT|SAMTOOLS_STATS' { - conda = 'bioconda::samtools bioconda::htslib' -} - -withName: 'SORTMERNA' { - conda = 'bioconda::sortmerna' -} - -withName: 'STAR_ALIGN|STAR_GENOMEGENERATE' { - conda = 'bioconda::star bioconda::samtools bioconda::htslib conda-forge::gawk' -} - -withName: 'STRINGTIE_STRINGTIE' { - conda = 'bioconda::stringtie' -} - -withName: 'SUBREAD_FEATURECOUNTS' { - conda = 'bioconda::subread' -} - -withName: 'SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT' { - conda = 'bioconda::bioconductor-summarizedexperiment' -} - -withName: 'TXIMETA_TXIMPORT' { - conda = 'bioconda::bioconductor-tximeta' -} - -withName: 'TRIMGALORE' { - conda = 'bioconda::trim-galore bioconda::cutadapt' -} - -withName: 'UCSC_BEDCLIP' { - conda = 'bioconda::ucsc-bedclip' -} - -withName: 'UCSC_BEDGRAPHTOBIGWIG' { - conda = 'bioconda::ucsc-bedgraphtobigwig' -} - -withName: 'UMITOOLS_DEDUP|UMITOOLS_EXTRACT|UMITOOLS_PREPAREFORRSEM' { - conda = 'bioconda::umi_tools' -} - -withName: 'UNTAR' { - conda = 'conda-forge::grep conda-forge::sed conda-forge::tar' -} - +process { + + // Apply software overrides for ARM compatibility + + withName: '.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' { + conda = 'seqera::star=2.6.1d bioconda::samtools conda-forge::gawk=5.1.0' + } + + withName: 'STAR_GENOMEGENERATE_IGENOMES' { + conda = 'bioconda::star bioconda::samtools conda-forge::gawk=5.1.0' + } + + withName: 'BBSPLIT' { + conda = 'bioconda::bbmap' + } + + withName: 'BEDTOOLS_GENOMECOV' { + conda = 'bioconda::bedtools' + } + + withName: 'CAT_FASTQ' { + conda = 'conda-forge::coreutils' + } + + withName: 'CAT_ADDITIONAL_FASTA' { + conda = 'conda-forge::python' + } + + withName: 'CUSTOM_GETCHROMSIZES' { + conda = 'bioconda::samtools' + } + + withName: 'CUSTOM_TX2GENE' { + conda = 'python' + } + + withName: 'DUPRADAR' { + conda = 'bioconda::bioconductor-dupradar' + } + + withName: 'FASTP' { + conda = 'bioconda::fastp' + } + + withName: 'FQ_SUBSAMPLE' { + conda = 'bioconda::fq' + } + + withName: 'GFFREAD' { + conda = 'bioconda::gffread' + } + + withName: 'GUNZIP' { + conda = 'conda-forge::sed' + } + + withName: 'HISAT2_ALIGN' { + conda = 'bioconda::hisat2 bioconda::samtools' + } + + withName: 'HISAT2_BUILD|HISAT2_EXTRACTSPLICESITES' { + conda = 'bioconda::hisat2' + } + + withName: 'KALLISTO_INDEX|KALLISTO_QUANT' { + conda = 'bioconda::kallisto' + } + + withName: 'MULTIQC' { + conda = 'bioconda::multiqc' + } + + withName: 'PICARD_MARKDUPLICATES' { + conda = 'bioconda::picard' + } + + withName: 'PRESEQ_LCEXTRAP' { + conda = 'bioconda::preseq' + } + + withName: 'QUALIMAP_RNASEQ' { + conda = 'bioconda::qualimap' + } + + withName: 'RSEM_CALCULATEEXPRESSION' { + conda = 'bioconda::rsem bioconda::star' + } + + withName: 'RSEM_PREPAREREFERENCE' { + conda = 'seqera::rsem seqera::star=2.6.1d' + } + + withName: 'RSEQC_BAMSTAT|RSEQC_INFEREXPERIMENT|RSEQC_INNERDISTANCE|RSEQC_JUNCTIONANNOTATION|RSEQC_JUNCTIONSATURATION|RSEQC_READDISTRIBUTION|RSEQC_READDUPLICATION|RSEQC_TIN' { + conda = 'bioconda::rseqc conda-forge::r-base' + } + + withName: 'SALMON_INDEX|SALMON_QUANT' { + conda = 'bioconda::salmon' + } + + withName: 'SAMTOOLS_FLAGSTAT|SAMTOOLS_IDXSTATS|SAMTOOLS_INDEX|SAMTOOLS_SORT|SAMTOOLS_STATS' { + conda = 'bioconda::samtools bioconda::htslib' + } + + withName: 'SORTMERNA' { + conda = 'bioconda::sortmerna' + } + + withName: 'STAR_ALIGN|STAR_GENOMEGENERATE' { + conda = 'bioconda::star bioconda::samtools bioconda::htslib conda-forge::gawk' + } + + withName: 'STRINGTIE_STRINGTIE' { + conda = 'bioconda::stringtie' + } + + withName: 'SUBREAD_FEATURECOUNTS' { + conda = 'bioconda::subread' + } + + withName: 'SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT' { + conda = 'bioconda::bioconductor-summarizedexperiment' + } + + withName: 'TXIMETA_TXIMPORT' { + conda = 'bioconda::bioconductor-tximeta' + } + + withName: 'TRIMGALORE' { + conda = 'bioconda::trim-galore bioconda::cutadapt' + } + + withName: 'UCSC_BEDCLIP' { + conda = 'bioconda::ucsc-bedclip' + } + + withName: 'UCSC_BEDGRAPHTOBIGWIG' { + conda = 'bioconda::ucsc-bedgraphtobigwig' + } + + withName: 'UMITOOLS_DEDUP|UMITOOLS_EXTRACT|UMITOOLS_PREPAREFORRSEM' { + conda = 'bioconda::umi_tools' + } + + withName: 'UNTAR' { + conda = 'conda-forge::grep conda-forge::sed conda-forge::tar' + } +} From f5208dd0e78762e51bb34740ecea16a5cfc40949 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Thu, 17 Oct 2024 16:31:04 +0100 Subject: [PATCH 07/18] note pins --- conf/arm.config | 76 ++++++++++++++++++++++++++++++++++++------------- 1 file changed, 56 insertions(+), 20 deletions(-) diff --git a/conf/arm.config b/conf/arm.config index 112cb66af..d5cbad5b4 100644 --- a/conf/arm.config +++ b/conf/arm.config @@ -3,146 +3,182 @@ process { // Apply software overrides for ARM compatibility withName: '.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' { - conda = 'seqera::star=2.6.1d bioconda::samtools conda-forge::gawk=5.1.0' + conda = 'seqera::star=2.6.1d bioconda::samtools=1.21 conda-forge::gawk=5.1.0' + //conda = 'seqera::star=2.6.1d bioconda::samtools=1.10 conda-forge::gawk=5.1.0' } withName: 'STAR_GENOMEGENERATE_IGENOMES' { - conda = 'bioconda::star bioconda::samtools conda-forge::gawk=5.1.0' + conda = 'bioconda::star bioconda::samtools=1.21 conda-forge::gawk=5.1.0' + //conda = 'seqera::star=2.6.1d bioconda::samtools=1.10 conda-forge::gawk=5.1.0' } withName: 'BBSPLIT' { - conda = 'bioconda::bbmap' + conda = 'bioconda::bbmap' + // conda = 'bioconda::bbmap=39.01' } withName: 'BEDTOOLS_GENOMECOV' { - conda = 'bioconda::bedtools' + conda = 'bioconda::bedtools::2.13.1' + //conda = 'bioconda::bedtools::2.13.1' } withName: 'CAT_FASTQ' { conda = 'conda-forge::coreutils' + //conda = 'conda-forge::coreutils=8.30' } withName: 'CAT_ADDITIONAL_FASTA' { conda = 'conda-forge::python' + //conda = 'conda-forge::coreutils=3.9.5' } withName: 'CUSTOM_GETCHROMSIZES' { - conda = 'bioconda::samtools' + conda = 'bioconda::samtools=1.21' + //conda = 'bioconda::samtools=1.20 bioconda::htslib=1.20' } withName: 'CUSTOM_TX2GENE' { - conda = 'python' + conda = 'python=3.13.0' + //conda = 'python=3.9.5' } withName: 'DUPRADAR' { - conda = 'bioconda::bioconductor-dupradar' + conda = 'bioconda::bioconductor-dupradar=1.32.0' + //conda = 'bioconda::bioconductor-dupradar=1.32.0' } withName: 'FASTP' { conda = 'bioconda::fastp' + //conda = 'bioconda::fastp=0.23.4' } withName: 'FQ_SUBSAMPLE' { conda = 'bioconda::fq' + //conda = 'bioconda::fq=0.9.1' } withName: 'GFFREAD' { conda = 'bioconda::gffread' + //conda = 'bioconda::gffread=0.12.7' } withName: 'GUNZIP' { conda = 'conda-forge::sed' + //conda = 'conda-forge::grep=3.11 conda-forge::sed=4.8 conda-forge::tar=1.34' } withName: 'HISAT2_ALIGN' { conda = 'bioconda::hisat2 bioconda::samtools' + //conda = 'bioconda::hisat2=2.2.1 bioconda::samtools=1.16.1' } withName: 'HISAT2_BUILD|HISAT2_EXTRACTSPLICESITES' { conda = 'bioconda::hisat2' + //conda = 'bioconda::hisat2=2.2.1' } withName: 'KALLISTO_INDEX|KALLISTO_QUANT' { conda = 'bioconda::kallisto' + //conda = 'bioconda::kallisto=0.48.0' } withName: 'MULTIQC' { - conda = 'bioconda::multiqc' + conda = 'bioconda::multiqc=1.25.1' + //conda = 'bioconda::multiqc=1.25.1' } withName: 'PICARD_MARKDUPLICATES' { - conda = 'bioconda::picard' + conda = 'bioconda::picard=3.3.0' + //conda = 'bioconda::picard=3.1.1' } withName: 'PRESEQ_LCEXTRAP' { conda = 'bioconda::preseq' + //conda = 'bioconda::preseq=3.1.2' } withName: 'QUALIMAP_RNASEQ' { - conda = 'bioconda::qualimap' + conda = 'bioconda::qualimap=2.3' + //conda = 'bioconda::qualimap=2.3' } withName: 'RSEM_CALCULATEEXPRESSION' { conda = 'bioconda::rsem bioconda::star' + //conda = 'bioconda::rsem=1.3.3 bioconda::star=2.7.10a' } withName: 'RSEM_PREPAREREFERENCE' { conda = 'seqera::rsem seqera::star=2.6.1d' + //conda = 'bioconda::rsem=1.3.3 bioconda::star=2.7.10a' } withName: 'RSEQC_BAMSTAT|RSEQC_INFEREXPERIMENT|RSEQC_INNERDISTANCE|RSEQC_JUNCTIONANNOTATION|RSEQC_JUNCTIONSATURATION|RSEQC_READDISTRIBUTION|RSEQC_READDUPLICATION|RSEQC_TIN' { - conda = 'bioconda::rseqc conda-forge::r-base' + conda = 'bioconda::rseqc=5.0.2 conda-forge::r-base' + //conda = 'bioconda::rseqc=5.0.3 conda-forge::r-base>=3.5' } withName: 'SALMON_INDEX|SALMON_QUANT' { - conda = 'bioconda::salmon' + conda = 'bioconda::salmon=1.10.3' + //conda = 'bioconda::salmon=1.10.1' } withName: 'SAMTOOLS_FLAGSTAT|SAMTOOLS_IDXSTATS|SAMTOOLS_INDEX|SAMTOOLS_SORT|SAMTOOLS_STATS' { - conda = 'bioconda::samtools bioconda::htslib' + conda = 'bioconda::samtools=1.21 bioconda::htslib' + //conda = 'bioconda::samtools=1.20 bioconda::htslib' } withName: 'SORTMERNA' { conda = 'bioconda::sortmerna' + //conda = 'bioconda::sortmerna=4.3.6' } withName: 'STAR_ALIGN|STAR_GENOMEGENERATE' { conda = 'bioconda::star bioconda::samtools bioconda::htslib conda-forge::gawk' + //conda = 'bioconda::star=2.7.10a bioconda::samtools=1.18 bioconda::htslib=1.18 conda-forge::gawk=5.1.0' } withName: 'STRINGTIE_STRINGTIE' { - conda = 'bioconda::stringtie' + conda = 'bioconda::stringtie=2.2.3' + //conda = 'bioconda::stringtie=2.2.1' } withName: 'SUBREAD_FEATURECOUNTS' { - conda = 'bioconda::subread' + conda = 'bioconda::subread=2.0.6' + //conda = 'bioconda::subread=2.0.1' } withName: 'SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT' { - conda = 'bioconda::bioconductor-summarizedexperiment' + conda = 'bioconda::bioconductor-summarizedexperiment=1.32.0' + //conda = 'bioconda::bioconductor-summarizedexperiment=1.32.0' } withName: 'TXIMETA_TXIMPORT' { - conda = 'bioconda::bioconductor-tximeta' + conda = 'bioconda::bioconductor-tximeta=1.20.1' + //conda = 'bioconda::bioconductor-tximeta=1.20.1' } withName: 'TRIMGALORE' { - conda = 'bioconda::trim-galore bioconda::cutadapt' + conda = 'bioconda::trim-galore=0.6.10 bioconda::cutadapt=4.9' + //conda = 'bioconda::trim-galore=0.6.7 bioconda::cutadapt=3.4' } withName: 'UCSC_BEDCLIP' { - conda = 'bioconda::ucsc-bedclip' + conda = 'bioconda::ucsc-bedclip=377' + //conda = 'bioconda::ucsc-bedclip=377' } withName: 'UCSC_BEDGRAPHTOBIGWIG' { - conda = 'bioconda::ucsc-bedgraphtobigwig' + conda = 'bioconda::ucsc-bedgraphtobigwig=445' + //conda = 'bioconda::ucsc-bedgraphtobigwig=445' } withName: 'UMITOOLS_DEDUP|UMITOOLS_EXTRACT|UMITOOLS_PREPAREFORRSEM' { conda = 'bioconda::umi_tools' + //conda = 'bioconda::umi_tools=1.1.5' } withName: 'UNTAR' { conda = 'conda-forge::grep conda-forge::sed conda-forge::tar' + //conda = 'conda-forge::grep=3.11 conda-forge::sed=4.8 conda-forge::tar=1.34' } } From ea8b9e8be4657416a3041351718493af03bfd410 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Thu, 17 Oct 2024 17:23:49 +0100 Subject: [PATCH 08/18] Remove conda overrides that were having no impact --- conf/arm.config | 40 ---------------------------------------- 1 file changed, 40 deletions(-) diff --git a/conf/arm.config b/conf/arm.config index d5cbad5b4..d73605e09 100644 --- a/conf/arm.config +++ b/conf/arm.config @@ -17,11 +17,6 @@ process { // conda = 'bioconda::bbmap=39.01' } - withName: 'BEDTOOLS_GENOMECOV' { - conda = 'bioconda::bedtools::2.13.1' - //conda = 'bioconda::bedtools::2.13.1' - } - withName: 'CAT_FASTQ' { conda = 'conda-forge::coreutils' //conda = 'conda-forge::coreutils=8.30' @@ -42,11 +37,6 @@ process { //conda = 'python=3.9.5' } - withName: 'DUPRADAR' { - conda = 'bioconda::bioconductor-dupradar=1.32.0' - //conda = 'bioconda::bioconductor-dupradar=1.32.0' - } - withName: 'FASTP' { conda = 'bioconda::fastp' //conda = 'bioconda::fastp=0.23.4' @@ -82,11 +72,6 @@ process { //conda = 'bioconda::kallisto=0.48.0' } - withName: 'MULTIQC' { - conda = 'bioconda::multiqc=1.25.1' - //conda = 'bioconda::multiqc=1.25.1' - } - withName: 'PICARD_MARKDUPLICATES' { conda = 'bioconda::picard=3.3.0' //conda = 'bioconda::picard=3.1.1' @@ -97,11 +82,6 @@ process { //conda = 'bioconda::preseq=3.1.2' } - withName: 'QUALIMAP_RNASEQ' { - conda = 'bioconda::qualimap=2.3' - //conda = 'bioconda::qualimap=2.3' - } - withName: 'RSEM_CALCULATEEXPRESSION' { conda = 'bioconda::rsem bioconda::star' //conda = 'bioconda::rsem=1.3.3 bioconda::star=2.7.10a' @@ -147,31 +127,11 @@ process { //conda = 'bioconda::subread=2.0.1' } - withName: 'SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT' { - conda = 'bioconda::bioconductor-summarizedexperiment=1.32.0' - //conda = 'bioconda::bioconductor-summarizedexperiment=1.32.0' - } - - withName: 'TXIMETA_TXIMPORT' { - conda = 'bioconda::bioconductor-tximeta=1.20.1' - //conda = 'bioconda::bioconductor-tximeta=1.20.1' - } - withName: 'TRIMGALORE' { conda = 'bioconda::trim-galore=0.6.10 bioconda::cutadapt=4.9' //conda = 'bioconda::trim-galore=0.6.7 bioconda::cutadapt=3.4' } - withName: 'UCSC_BEDCLIP' { - conda = 'bioconda::ucsc-bedclip=377' - //conda = 'bioconda::ucsc-bedclip=377' - } - - withName: 'UCSC_BEDGRAPHTOBIGWIG' { - conda = 'bioconda::ucsc-bedgraphtobigwig=445' - //conda = 'bioconda::ucsc-bedgraphtobigwig=445' - } - withName: 'UMITOOLS_DEDUP|UMITOOLS_EXTRACT|UMITOOLS_PREPAREFORRSEM' { conda = 'bioconda::umi_tools' //conda = 'bioconda::umi_tools=1.1.5' From db02d992556f593a66b0d5da9718f519bb2934f0 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 18 Oct 2024 09:45:44 +0100 Subject: [PATCH 09/18] Use different RSEQC pin --- conf/arm.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/arm.config b/conf/arm.config index d73605e09..f8e288f9d 100644 --- a/conf/arm.config +++ b/conf/arm.config @@ -93,7 +93,7 @@ process { } withName: 'RSEQC_BAMSTAT|RSEQC_INFEREXPERIMENT|RSEQC_INNERDISTANCE|RSEQC_JUNCTIONANNOTATION|RSEQC_JUNCTIONSATURATION|RSEQC_READDISTRIBUTION|RSEQC_READDUPLICATION|RSEQC_TIN' { - conda = 'bioconda::rseqc=5.0.2 conda-forge::r-base' + conda = 'bioconda::rseqc=5.0.4 conda-forge::r-base' //conda = 'bioconda::rseqc=5.0.3 conda-forge::r-base>=3.5' } From 4a8ed2bb00bff13cdef9f4470c4a95bead441542 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 18 Oct 2024 10:28:04 +0100 Subject: [PATCH 10/18] update BEDGRAPHTOBIGWIG pin --- conf/arm.config | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/conf/arm.config b/conf/arm.config index f8e288f9d..4f7772681 100644 --- a/conf/arm.config +++ b/conf/arm.config @@ -131,6 +131,11 @@ process { conda = 'bioconda::trim-galore=0.6.10 bioconda::cutadapt=4.9' //conda = 'bioconda::trim-galore=0.6.7 bioconda::cutadapt=3.4' } + + withName: 'UCSC_BEDGRAPHTOBIGWIG' { + conda = 'bioconda::ucsc-bedgraphtobigwig=469' + //conda = 'bioconda::ucsc-bedgraphtobigwig=469' + } withName: 'UMITOOLS_DEDUP|UMITOOLS_EXTRACT|UMITOOLS_PREPAREFORRSEM' { conda = 'bioconda::umi_tools' From b86a6f9d9fc3515865eb4aaa600882df6c893c80 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 18 Oct 2024 10:37:14 +0100 Subject: [PATCH 11/18] Fix annotation --- conf/arm.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/arm.config b/conf/arm.config index 4f7772681..4efeabdfe 100644 --- a/conf/arm.config +++ b/conf/arm.config @@ -133,7 +133,7 @@ process { } withName: 'UCSC_BEDGRAPHTOBIGWIG' { - conda = 'bioconda::ucsc-bedgraphtobigwig=469' + conda = 'bioconda::ucsc-bedgraphtobigwig=445' //conda = 'bioconda::ucsc-bedgraphtobigwig=469' } From 1b96eb886b80c4cba0691728a89a4f17dbc5a0ec Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 18 Oct 2024 10:47:36 +0100 Subject: [PATCH 12/18] Don't think we need the RSEQC pin --- conf/arm.config | 5 ----- 1 file changed, 5 deletions(-) diff --git a/conf/arm.config b/conf/arm.config index 4efeabdfe..37a6d1211 100644 --- a/conf/arm.config +++ b/conf/arm.config @@ -92,11 +92,6 @@ process { //conda = 'bioconda::rsem=1.3.3 bioconda::star=2.7.10a' } - withName: 'RSEQC_BAMSTAT|RSEQC_INFEREXPERIMENT|RSEQC_INNERDISTANCE|RSEQC_JUNCTIONANNOTATION|RSEQC_JUNCTIONSATURATION|RSEQC_READDISTRIBUTION|RSEQC_READDUPLICATION|RSEQC_TIN' { - conda = 'bioconda::rseqc=5.0.4 conda-forge::r-base' - //conda = 'bioconda::rseqc=5.0.3 conda-forge::r-base>=3.5' - } - withName: 'SALMON_INDEX|SALMON_QUANT' { conda = 'bioconda::salmon=1.10.3' //conda = 'bioconda::salmon=1.10.1' From 4e5d7a38d2c6fe355eaebde60611ec4c5b21f188 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 18 Oct 2024 14:26:45 +0100 Subject: [PATCH 13/18] correct ucsc --- conf/arm.config | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/conf/arm.config b/conf/arm.config index 37a6d1211..933dfc928 100644 --- a/conf/arm.config +++ b/conf/arm.config @@ -128,8 +128,8 @@ process { } withName: 'UCSC_BEDGRAPHTOBIGWIG' { - conda = 'bioconda::ucsc-bedgraphtobigwig=445' - //conda = 'bioconda::ucsc-bedgraphtobigwig=469' + conda = 'bioconda::ucsc-bedgraphtobigwig=469' + //conda = 'bioconda::ucsc-bedgraphtobigwig=445' } withName: 'UMITOOLS_DEDUP|UMITOOLS_EXTRACT|UMITOOLS_PREPAREFORRSEM' { From 902367e6cb02990d70c1583bf52ec6ecb70f3b91 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 18 Oct 2024 20:25:21 +0100 Subject: [PATCH 14/18] Triage arm deps --- conf/arm.config | 229 +++++++++++++++++++++++++----------------------- 1 file changed, 121 insertions(+), 108 deletions(-) diff --git a/conf/arm.config b/conf/arm.config index 933dfc928..4a6f22e53 100644 --- a/conf/arm.config +++ b/conf/arm.config @@ -1,144 +1,157 @@ process { + // // Apply software overrides for ARM compatibility - - withName: '.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' { - conda = 'seqera::star=2.6.1d bioconda::samtools=1.21 conda-forge::gawk=5.1.0' - //conda = 'seqera::star=2.6.1d bioconda::samtools=1.10 conda-forge::gawk=5.1.0' - } - - withName: 'STAR_GENOMEGENERATE_IGENOMES' { - conda = 'bioconda::star bioconda::samtools=1.21 conda-forge::gawk=5.1.0' - //conda = 'seqera::star=2.6.1d bioconda::samtools=1.10 conda-forge::gawk=5.1.0' - } - - withName: 'BBSPLIT' { - conda = 'bioconda::bbmap' - // conda = 'bioconda::bbmap=39.01' - } - - withName: 'CAT_FASTQ' { - conda = 'conda-forge::coreutils' - //conda = 'conda-forge::coreutils=8.30' - } - - withName: 'CAT_ADDITIONAL_FASTA' { - conda = 'conda-forge::python' - //conda = 'conda-forge::coreutils=3.9.5' - } - + // + + //// Tested, working, module updates in progress on main dev branch + withName: 'CUSTOM_GETCHROMSIZES' { conda = 'bioconda::samtools=1.21' //conda = 'bioconda::samtools=1.20 bioconda::htslib=1.20' } - + withName: 'CUSTOM_TX2GENE' { conda = 'python=3.13.0' //conda = 'python=3.9.5' } - - withName: 'FASTP' { - conda = 'bioconda::fastp' - //conda = 'bioconda::fastp=0.23.4' - } - - withName: 'FQ_SUBSAMPLE' { - conda = 'bioconda::fq' - //conda = 'bioconda::fq=0.9.1' - } - - withName: 'GFFREAD' { - conda = 'bioconda::gffread' - //conda = 'bioconda::gffread=0.12.7' - } - - withName: 'GUNZIP' { - conda = 'conda-forge::sed' - //conda = 'conda-forge::grep=3.11 conda-forge::sed=4.8 conda-forge::tar=1.34' - } - - withName: 'HISAT2_ALIGN' { - conda = 'bioconda::hisat2 bioconda::samtools' - //conda = 'bioconda::hisat2=2.2.1 bioconda::samtools=1.16.1' - } - - withName: 'HISAT2_BUILD|HISAT2_EXTRACTSPLICESITES' { - conda = 'bioconda::hisat2' - //conda = 'bioconda::hisat2=2.2.1' - } - - withName: 'KALLISTO_INDEX|KALLISTO_QUANT' { - conda = 'bioconda::kallisto' - //conda = 'bioconda::kallisto=0.48.0' - } - - withName: 'PICARD_MARKDUPLICATES' { - conda = 'bioconda::picard=3.3.0' - //conda = 'bioconda::picard=3.1.1' - } - - withName: 'PRESEQ_LCEXTRAP' { - conda = 'bioconda::preseq' - //conda = 'bioconda::preseq=3.1.2' - } - - withName: 'RSEM_CALCULATEEXPRESSION' { - conda = 'bioconda::rsem bioconda::star' - //conda = 'bioconda::rsem=1.3.3 bioconda::star=2.7.10a' - } - - withName: 'RSEM_PREPAREREFERENCE' { - conda = 'seqera::rsem seqera::star=2.6.1d' - //conda = 'bioconda::rsem=1.3.3 bioconda::star=2.7.10a' - } - + withName: 'SALMON_INDEX|SALMON_QUANT' { conda = 'bioconda::salmon=1.10.3' //conda = 'bioconda::salmon=1.10.1' } - + withName: 'SAMTOOLS_FLAGSTAT|SAMTOOLS_IDXSTATS|SAMTOOLS_INDEX|SAMTOOLS_SORT|SAMTOOLS_STATS' { conda = 'bioconda::samtools=1.21 bioconda::htslib' //conda = 'bioconda::samtools=1.20 bioconda::htslib' } - - withName: 'SORTMERNA' { - conda = 'bioconda::sortmerna' - //conda = 'bioconda::sortmerna=4.3.6' - } - - withName: 'STAR_ALIGN|STAR_GENOMEGENERATE' { - conda = 'bioconda::star bioconda::samtools bioconda::htslib conda-forge::gawk' - //conda = 'bioconda::star=2.7.10a bioconda::samtools=1.18 bioconda::htslib=1.18 conda-forge::gawk=5.1.0' + + withName: 'TRIMGALORE' { + conda = 'bioconda::trim-galore=0.6.10 bioconda::cutadapt=4.9' + //conda = 'bioconda::trim-galore=0.6.7 bioconda::cutadapt=3.4' } - + withName: 'STRINGTIE_STRINGTIE' { conda = 'bioconda::stringtie=2.2.3' //conda = 'bioconda::stringtie=2.2.1' } - + withName: 'SUBREAD_FEATURECOUNTS' { conda = 'bioconda::subread=2.0.6' //conda = 'bioconda::subread=2.0.1' } - - withName: 'TRIMGALORE' { - conda = 'bioconda::trim-galore=0.6.10 bioconda::cutadapt=4.9' - //conda = 'bioconda::trim-galore=0.6.7 bioconda::cutadapt=3.4' - } withName: 'UCSC_BEDGRAPHTOBIGWIG' { conda = 'bioconda::ucsc-bedgraphtobigwig=469' //conda = 'bioconda::ucsc-bedgraphtobigwig=445' } - - withName: 'UMITOOLS_DEDUP|UMITOOLS_EXTRACT|UMITOOLS_PREPAREFORRSEM' { - conda = 'bioconda::umi_tools' - //conda = 'bioconda::umi_tools=1.1.5' + + //// Untested, but have aarch conda builds in bioconda/ conda-forge channels. + //// Should update the nf-core modules + + withName: 'BBSPLIT' { + conda = 'bioconda::bbmap=39.10' + // conda = 'bioconda::bbmap=39.01' + } + + withName: 'CAT_FASTQ' { + conda = 'conda-forge::coreutils=9.5' + //conda = 'conda-forge::coreutils=8.30' + } + + withName: 'CAT_ADDITIONAL_FASTA' { + conda = 'python=3.13.0' + //conda = 'conda-forge::coreutils=3.9.5' + } + + withName: 'FQ_SUBSAMPLE' { + conda = 'bioconda::fq=0.12.0' + //conda = 'bioconda::fq=0.9.1' } + + withName: 'KALLISTO_INDEX|KALLISTO_QUANT' { + conda = 'bioconda::kallisto=0.51.1' + //conda = 'bioconda::kallisto=0.48.0' + } + + withName: 'PRESEQ_LCEXTRAP' { + conda = 'bioconda::preseq=3.2.0' + //conda = 'bioconda::preseq=3.1.2' + } + + withName: 'SORTMERNA' { + conda = 'bioconda::sortmerna=4.3.7' + //conda = 'bioconda::sortmerna=4.3.6' + } + + //// No longer necessary- dev branch version has an aarch 64 build (s) + + //withName: 'GUNZIP' { + // conda = 'conda-forge::sed' + // //conda = 'conda-forge::grep=3.11 conda-forge::sed=4.8 conda-forge::tar=1.34' + //} + + //withName: 'UNTAR' { + // conda = 'conda-forge::grep conda-forge::sed conda-forge::tar' + // //conda = 'conda-forge::grep=3.11 conda-forge::sed=4.8 conda-forge::tar=1.34' + //} + + //withName: 'FASTP' { + // conda = 'bioconda::fastp' + // //conda = 'bioconda::fastp=0.23.4' + //} + + //withName: 'GFFREAD' { + // conda = 'bioconda::gffread' + // //conda = 'bioconda::gffread=0.12.7' + //} + + //withName: 'UMITOOLS_DEDUP|UMITOOLS_EXTRACT|UMITOOLS_PREPAREFORRSEM' { + // conda = 'bioconda::umi_tools' + // //conda = 'bioconda::umi_tools=1.1.5' + //} + + //// No aarch64 builds in bioconda / conda-forge channels + + //// a) have seqera aarch64 conda builds - withName: 'UNTAR' { - conda = 'conda-forge::grep conda-forge::sed conda-forge::tar' - //conda = 'conda-forge::grep=3.11 conda-forge::sed=4.8 conda-forge::tar=1.34' + withName: '.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' { + conda = 'seqera::star=2.6.1d bioconda::samtools=1.21 conda-forge::gawk=5.1.0' + //conda = 'seqera::star=2.6.1d bioconda::samtools=1.10 conda-forge::gawk=5.1.0' + } + + withName: 'STAR_GENOMEGENERATE_IGENOMES' { + conda = 'seqera::star=2.6.1d bioconda::samtools=1.21 conda-forge::gawk=5.1.0' + //conda = 'bioconda::star=2.6.1d bioconda::samtools=1.10 conda-forge::gawk=5.1.0' } -} + + withName: 'RSEM_PREPAREREFERENCE' { + conda = 'seqera::rsem=1.3.3 seqera::star=2.6.1d' + //conda = 'bioconda::rsem=1.3.3 bioconda::star=2.7.10a' + } + + withName: 'RSEM_CALCULATEEXPRESSION' { + conda = 'seqera::rsem=1.3.3 seqera::star=2.6.1d' + //conda = 'bioconda::rsem=1.3.3 bioconda::star=2.7.10a' + } + + // NOTE THE OLDER STAR VERSION HERE! + + withName: 'STAR_ALIGN|STAR_GENOMEGENERATE' { + conda = 'seqera::star2.6.1d bioconda::samtools=1.21 bioconda::htslib=1.21 conda-forge::gawk=5.1.0' + //conda = 'bioconda::star=2.7.10a bioconda::samtools=1.18 bioconda::htslib=1.18 conda-forge::gawk=5.1.0' + } + + //// b) need aarch64 conda builds + + //withName: 'HISAT2_ALIGN' { + // conda = 'bioconda::hisat2 bioconda::samtools' + // //conda = 'bioconda::hisat2=2.2.1 bioconda::samtools=1.16.1' + //} + + //withName: 'HISAT2_BUILD|HISAT2_EXTRACTSPLICESITES' { + // conda = 'bioconda::hisat2' + // //conda = 'bioconda::hisat2=2.2.1' + //} + +} From 328d02d1bd2c80c55743d804bc6e13db207fd66b Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 18 Oct 2024 20:32:03 +0100 Subject: [PATCH 15/18] Non-igenomes STAR can use the latest star --- conf/arm.config | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/conf/arm.config b/conf/arm.config index 4a6f22e53..801473fa6 100644 --- a/conf/arm.config +++ b/conf/arm.config @@ -83,6 +83,11 @@ process { conda = 'bioconda::sortmerna=4.3.7' //conda = 'bioconda::sortmerna=4.3.6' } + + withName: 'STAR_ALIGN|STAR_GENOMEGENERATE' { + conda = 'seqera::star2.7.11b bioconda::samtools=1.21 bioconda::htslib=1.21 conda-forge::gawk=5.1.0' + //conda = 'bioconda::star=2.7.10a bioconda::samtools=1.18 bioconda::htslib=1.18 conda-forge::gawk=5.1.0' + } //// No longer necessary- dev branch version has an aarch 64 build (s) @@ -137,11 +142,6 @@ process { // NOTE THE OLDER STAR VERSION HERE! - withName: 'STAR_ALIGN|STAR_GENOMEGENERATE' { - conda = 'seqera::star2.6.1d bioconda::samtools=1.21 bioconda::htslib=1.21 conda-forge::gawk=5.1.0' - //conda = 'bioconda::star=2.7.10a bioconda::samtools=1.18 bioconda::htslib=1.18 conda-forge::gawk=5.1.0' - } - //// b) need aarch64 conda builds //withName: 'HISAT2_ALIGN' { From 2f92bfc2199e93ac8747128726130a09cb331544 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 18 Oct 2024 20:44:00 +0100 Subject: [PATCH 16/18] remove rogue comment --- conf/arm.config | 2 -- 1 file changed, 2 deletions(-) diff --git a/conf/arm.config b/conf/arm.config index 801473fa6..55547a6fe 100644 --- a/conf/arm.config +++ b/conf/arm.config @@ -140,8 +140,6 @@ process { //conda = 'bioconda::rsem=1.3.3 bioconda::star=2.7.10a' } - // NOTE THE OLDER STAR VERSION HERE! - //// b) need aarch64 conda builds //withName: 'HISAT2_ALIGN' { From 0a563dcedf654ac152ae04e8f4f10f97a5251335 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 21 Oct 2024 11:58:41 +0100 Subject: [PATCH 17/18] update arm conf --- conf/arm.config | 73 ++++++++++++++++++------------------------------- 1 file changed, 26 insertions(+), 47 deletions(-) diff --git a/conf/arm.config b/conf/arm.config index 55547a6fe..4a56788fe 100644 --- a/conf/arm.config +++ b/conf/arm.config @@ -45,25 +45,12 @@ process { conda = 'bioconda::ucsc-bedgraphtobigwig=469' //conda = 'bioconda::ucsc-bedgraphtobigwig=445' } - - //// Untested, but have aarch conda builds in bioconda/ conda-forge channels. - //// Should update the nf-core modules - + withName: 'BBSPLIT' { conda = 'bioconda::bbmap=39.10' // conda = 'bioconda::bbmap=39.01' } - withName: 'CAT_FASTQ' { - conda = 'conda-forge::coreutils=9.5' - //conda = 'conda-forge::coreutils=8.30' - } - - withName: 'CAT_ADDITIONAL_FASTA' { - conda = 'python=3.13.0' - //conda = 'conda-forge::coreutils=3.9.5' - } - withName: 'FQ_SUBSAMPLE' { conda = 'bioconda::fq=0.12.0' //conda = 'bioconda::fq=0.9.1' @@ -73,48 +60,32 @@ process { conda = 'bioconda::kallisto=0.51.1' //conda = 'bioconda::kallisto=0.48.0' } - + withName: 'PRESEQ_LCEXTRAP' { conda = 'bioconda::preseq=3.2.0' //conda = 'bioconda::preseq=3.1.2' } - - withName: 'SORTMERNA' { - conda = 'bioconda::sortmerna=4.3.7' - //conda = 'bioconda::sortmerna=4.3.6' - } - withName: 'STAR_ALIGN|STAR_GENOMEGENERATE' { - conda = 'seqera::star2.7.11b bioconda::samtools=1.21 bioconda::htslib=1.21 conda-forge::gawk=5.1.0' - //conda = 'bioconda::star=2.7.10a bioconda::samtools=1.18 bioconda::htslib=1.18 conda-forge::gawk=5.1.0' + withName: 'CAT_ADDITIONAL_FASTA' { + conda = 'python=3.13.0' + //conda = 'conda-forge::coreutils=3.9.5' } - //// No longer necessary- dev branch version has an aarch 64 build (s) - - //withName: 'GUNZIP' { - // conda = 'conda-forge::sed' - // //conda = 'conda-forge::grep=3.11 conda-forge::sed=4.8 conda-forge::tar=1.34' - //} - - //withName: 'UNTAR' { - // conda = 'conda-forge::grep conda-forge::sed conda-forge::tar' - // //conda = 'conda-forge::grep=3.11 conda-forge::sed=4.8 conda-forge::tar=1.34' - //} - - //withName: 'FASTP' { - // conda = 'bioconda::fastp' - // //conda = 'bioconda::fastp=0.23.4' - //} + //// Proposed to nf-core with Seqera container + + // Seqera container, since coreutils in existing image (ubuntu) wouldn't + // match update + withName: 'CAT_FASTQ' { + conda = 'conda-forge::coreutils=9.5' + //conda = 'conda-forge::coreutils=8.30' + } - //withName: 'GFFREAD' { - // conda = 'bioconda::gffread' - // //conda = 'bioconda::gffread=0.12.7' - //} + // Seqera container to avoid updating a mulled container - //withName: 'UMITOOLS_DEDUP|UMITOOLS_EXTRACT|UMITOOLS_PREPAREFORRSEM' { - // conda = 'bioconda::umi_tools' - // //conda = 'bioconda::umi_tools=1.1.5' - //} + withName: 'STAR_ALIGN|STAR_GENOMEGENERATE' { + conda = 'bioconda::star2.7.11b bioconda::samtools=1.21 bioconda::htslib=1.21 conda-forge::gawk=5.1.0' + //conda = 'bioconda::star=2.7.10a bioconda::samtools=1.18 bioconda::htslib=1.18 conda-forge::gawk=5.1.0' + } //// No aarch64 builds in bioconda / conda-forge channels @@ -152,4 +123,12 @@ process { // //conda = 'bioconda::hisat2=2.2.1' //} + //// c) have aarch64 builds in bioconda, but with problems + // sortmerna gives 'illegal instruction' errors at 5.3.7 with either + // Biocontainers or Seqera Containers + withName: 'SORTMERNA' { + conda = 'bioconda::sortmerna=4.3.7' + //conda = 'bioconda::sortmerna=4.3.6' + } + } From 0be2d6a53fb70c2f8afc7ce55debdea68eb30b6e Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Tue, 22 Oct 2024 14:02:56 +0100 Subject: [PATCH 18/18] Cut out module redundant software overrides --- conf/arm.config | 95 ------------------------------------------------- 1 file changed, 95 deletions(-) diff --git a/conf/arm.config b/conf/arm.config index 4a56788fe..cfcd283fa 100644 --- a/conf/arm.config +++ b/conf/arm.config @@ -1,92 +1,5 @@ process { - // - // Apply software overrides for ARM compatibility - // - - //// Tested, working, module updates in progress on main dev branch - - withName: 'CUSTOM_GETCHROMSIZES' { - conda = 'bioconda::samtools=1.21' - //conda = 'bioconda::samtools=1.20 bioconda::htslib=1.20' - } - - withName: 'CUSTOM_TX2GENE' { - conda = 'python=3.13.0' - //conda = 'python=3.9.5' - } - - withName: 'SALMON_INDEX|SALMON_QUANT' { - conda = 'bioconda::salmon=1.10.3' - //conda = 'bioconda::salmon=1.10.1' - } - - withName: 'SAMTOOLS_FLAGSTAT|SAMTOOLS_IDXSTATS|SAMTOOLS_INDEX|SAMTOOLS_SORT|SAMTOOLS_STATS' { - conda = 'bioconda::samtools=1.21 bioconda::htslib' - //conda = 'bioconda::samtools=1.20 bioconda::htslib' - } - - withName: 'TRIMGALORE' { - conda = 'bioconda::trim-galore=0.6.10 bioconda::cutadapt=4.9' - //conda = 'bioconda::trim-galore=0.6.7 bioconda::cutadapt=3.4' - } - - withName: 'STRINGTIE_STRINGTIE' { - conda = 'bioconda::stringtie=2.2.3' - //conda = 'bioconda::stringtie=2.2.1' - } - - withName: 'SUBREAD_FEATURECOUNTS' { - conda = 'bioconda::subread=2.0.6' - //conda = 'bioconda::subread=2.0.1' - } - - withName: 'UCSC_BEDGRAPHTOBIGWIG' { - conda = 'bioconda::ucsc-bedgraphtobigwig=469' - //conda = 'bioconda::ucsc-bedgraphtobigwig=445' - } - - withName: 'BBSPLIT' { - conda = 'bioconda::bbmap=39.10' - // conda = 'bioconda::bbmap=39.01' - } - - withName: 'FQ_SUBSAMPLE' { - conda = 'bioconda::fq=0.12.0' - //conda = 'bioconda::fq=0.9.1' - } - - withName: 'KALLISTO_INDEX|KALLISTO_QUANT' { - conda = 'bioconda::kallisto=0.51.1' - //conda = 'bioconda::kallisto=0.48.0' - } - - withName: 'PRESEQ_LCEXTRAP' { - conda = 'bioconda::preseq=3.2.0' - //conda = 'bioconda::preseq=3.1.2' - } - - withName: 'CAT_ADDITIONAL_FASTA' { - conda = 'python=3.13.0' - //conda = 'conda-forge::coreutils=3.9.5' - } - - //// Proposed to nf-core with Seqera container - - // Seqera container, since coreutils in existing image (ubuntu) wouldn't - // match update - withName: 'CAT_FASTQ' { - conda = 'conda-forge::coreutils=9.5' - //conda = 'conda-forge::coreutils=8.30' - } - - // Seqera container to avoid updating a mulled container - - withName: 'STAR_ALIGN|STAR_GENOMEGENERATE' { - conda = 'bioconda::star2.7.11b bioconda::samtools=1.21 bioconda::htslib=1.21 conda-forge::gawk=5.1.0' - //conda = 'bioconda::star=2.7.10a bioconda::samtools=1.18 bioconda::htslib=1.18 conda-forge::gawk=5.1.0' - } - //// No aarch64 builds in bioconda / conda-forge channels //// a) have seqera aarch64 conda builds @@ -123,12 +36,4 @@ process { // //conda = 'bioconda::hisat2=2.2.1' //} - //// c) have aarch64 builds in bioconda, but with problems - // sortmerna gives 'illegal instruction' errors at 5.3.7 with either - // Biocontainers or Seqera Containers - withName: 'SORTMERNA' { - conda = 'bioconda::sortmerna=4.3.7' - //conda = 'bioconda::sortmerna=4.3.6' - } - }