Make genomic FASTA input optional #235
GitHub Actions / JUnit Test Report
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Jan 21, 2025 in 0s
2 tests run, 0 passed, 0 skipped, 2 failed.
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Check failure on line 1 in Test pipeline with Salmon, skipping both QC and alignment
github-actions / JUnit Test Report
Test pipeline with Salmon, skipping both QC and alignment.Params: --pseudo_aligner salmon --skip_qc --skip_alignment
Assertion failed:
2 of 2 assertions failed
Raw output
Nextflow stdout:
N E X T F L O W ~ version 24.12.0-edge
Launching `/home/runner/work/rnaseq/rnaseq/tests/../main.nf` [suspicious_gates] DSL2 - revision: 85c9b75b8b
Downloading plugin [email protected]
-[2m----------------------------------------------------[0m-
[0;32m,--.[0;30m/[0;32m,-.[0m
[0;34m ___ __ __ __ ___ [0;32m/,-._.--~'[0m
[0;34m |\ | |__ __ / ` / \ |__) |__ [0;33m} {[0m
[0;34m | \| | \__, \__/ | \ |___ [0;32m\`-._,-`-,[0m
[0;32m`._,._,'[0m
[0;35m nf-core/rnaseq 3.19.0dev[0m
-[2m----------------------------------------------------[0m-
[1mInput/output options[0m
[0;34minput : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/samplesheet/v3.10/samplesheet_test.csv[0m
[0;34moutdir : [0;32m/home/runner/work/rnaseq/rnaseq/~/tests/2c97d6a7ef1fd209d075664ba337cec3/output[0m
[1mReference genome options[0m
[0;34mfasta : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/genome.fasta[0m
[0;34mgtf : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/genes_with_empty_tid.gtf.gz[0m
[0;34mgff : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/genes.gff.gz[0m
[0;34mtranscript_fasta : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/transcriptome.fasta[0m
[0;34madditional_fasta : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/gfp.fa.gz[0m
[0;34mhisat2_index : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/hisat2.tar.gz[0m
[0;34mrsem_index : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/rsem.tar.gz[0m
[0;34msalmon_index : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/salmon.tar.gz[0m
[0;34mhisat2_build_memory : [0;32m3.GB[0m
[1mRead filtering options[0m
[0;34mbbsplit_fasta_list : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/bbsplit_fasta_list.txt[0m
[1mUMI options[0m
[0;34mumitools_bc_pattern : [0;32mNNNN[0m
[1mAlignment options[0m
[0;34mpseudo_aligner : [0;32msalmon[0m
[1mProcess skipping options[0m
[0;34mskip_bbsplit : [0;32mfalse[0m
[0;34mskip_alignment : [0;32mtrue[0m
[0;34mskip_qc : [0;32mtrue[0m
[1mInstitutional config options[0m
[0;34mconfig_profile_name : [0;32mTest profile[0m
[0;34mconfig_profile_description : [0;32mMinimal test dataset to check pipeline function[0m
[1mGeneric options[0m
[0;34mpipelines_testdata_base_path: [0;32ms3://ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/[0m
[1mCore Nextflow options[0m
[0;34mrunName : [0;32msuspicious_gates[0m
[0;34mcontainerEngine : [0;32mdocker[0m
[0;34mlaunchDir : [0;32m/home/runner/work/rnaseq/rnaseq/~/tests/2c97d6a7ef1fd209d075664ba337cec3[0m
[0;34mworkDir : [0;32m/home/runner/work/rnaseq/rnaseq/~/tests/2c97d6a7ef1fd209d075664ba337cec3/work[0m
[0;34mprojectDir : [0;32m/home/runner/work/rnaseq/rnaseq[0m
[0;34muserName : [0;32mrunner[0m
[0;34mprofile : [0;32mtest,docker[0m
[0;34mconfigFiles : [0;32m[0m
!! Only displaying parameters that differ from the pipeline defaults !!
-[2m----------------------------------------------------[0m-
* The pipeline
https://doi.org/10.5281/zenodo.1400710
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
https://github.com/nf-core/rnaseq/blob/master/CITATIONS.md
WARN: The following invalid input values have been detected:
* --modules_testdata_base_path: s3://ngi-igenomes/testdata/nf-core/modules/
WARN: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Both '--gtf' and '--gff' parameters have been provided.
Using GTF file as priority.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
WARN: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
'--transcript_fasta' parameter has been provided.
Make sure transcript names in this file match those in the GFF/GTF file.
Please see:
https://github.com/nf-core/rnaseq/issues/753
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
WARN: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
'--skip_alignment' parameter has been provided.
Skipping alignment, genome-based quantification and all downstream QC processes.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition
[78/bbd38d] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (RAP1_UNINDUCED_REP1)
[fe/b16bab] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)
[df/217507] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (RAP1_UNINDUCED_REP1)
ERROR ~ Error executing process > 'NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (RAP1_UNINDUCED_REP1)'
Caused by:
Process `NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (RAP1_UNINDUCED_REP1)` terminated with an error exit status (126)
Command executed:
fq lint \
--disable-validator P001 \
SRR6357073_1.fastq.gz > RAP1_UNINDUCED_REP1.fq_lint.txt
cat <<-END_VERSIONS > versions.yml
"NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT":
fq: $(echo $(fq lint --version | sed 's/fq-lint //g'))
END_VERSIONS
Command exit status:
126
Command output:
(empty)
Command error:
Unable to find image 'quay.io/biocontainers/fq:0.12.0--h9ee0642_0' locally
0.12.0--h9ee0642_0: Pulling from biocontainers/fq
0cacab098358: Pulling fs layer
bd9ddc54bea9: Pulling fs layer
71ed848086ad: Pulling fs layer
0cacab098358: Verifying Checksum
0cacab098358: Download complete
71ed848086ad: Verifying Checksum
71ed848086ad: Download complete
0cacab098358: Pull complete
bd9ddc54bea9: Pull complete
71ed848086ad: Pull complete
Digest: sha256:74b59572f1d05b4829b45b599ee04311c8b3acec510f3cfb879f23b4bbd2090b
Status: Downloaded newer image for quay.io/biocontainers/fq:0.12.0--h9ee0642_0
/bin/bash: line 10: .command.run: Permission denied
Work dir:
/home/runner/work/rnaseq/rnaseq/~/tests/2c97d6a7ef1fd209d075664ba337cec3/work/78/bbd38d161f392be3139e99564800c6
Container:
quay.io/biocontainers/fq:0.12.0--h9ee0642_0
Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`
-- Check '/home/runner/work/rnaseq/rnaseq/~/tests/2c97d6a7ef1fd209d075664ba337cec3/meta/nextflow.log' file for details
Execution cancelled -- Finishing pending tasks before exit
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting
-- Check '/home/runner/work/rnaseq/rnaseq/~/tests/2c97d6a7ef1fd209d075664ba337cec3/meta/nextflow.log' file for details
ERROR ~ Cannot invoke "java.nio.file.Path.getFileSystem()" because "path" is null
-- Check script '/home/runner/work/rnaseq/rnaseq/./workflows/rnaseq/../../subworkflows/nf-core/utils_nfcore_pipeline/main.nf' at line: 97 or see '/home/runner/work/rnaseq/rnaseq/~/tests/2c97d6a7ef1fd209d075664ba337cec3/meta/nextflow.log' file for more details
WARN: Got an interrupted exception while taking agent result | java.lang.InterruptedException
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting
-- Check '/home/runner/work/rnaseq/rnaseq/~/tests/2c97d6a7ef1fd209d075664ba337cec3/meta/nextflow.log' file for details
-[0;35m[nf-core/rnaseq][0;31m Pipeline completed with errors[0m-
WARN: Killing running tasks (2)
Nextflow stderr:
Check failure on line 1 in Test pipeline with Salmon, skipping both QC and alignment
github-actions / JUnit Test Report
Test pipeline with Salmon, skipping both QC and alignment.Params: --pseudo_aligner salmon --skip_qc --skip_alignment - stub
Assertion failed:
2 of 2 assertions failed
Raw output
Nextflow stdout:
N E X T F L O W ~ version 24.12.0-edge
Launching `/home/runner/work/rnaseq/rnaseq/tests/../main.nf` [zen_faraday] DSL2 - revision: 85c9b75b8b
-[2m----------------------------------------------------[0m-
[0;32m,--.[0;30m/[0;32m,-.[0m
[0;34m ___ __ __ __ ___ [0;32m/,-._.--~'[0m
[0;34m |\ | |__ __ / ` / \ |__) |__ [0;33m} {[0m
[0;34m | \| | \__, \__/ | \ |___ [0;32m\`-._,-`-,[0m
[0;32m`._,._,'[0m
[0;35m nf-core/rnaseq 3.19.0dev[0m
-[2m----------------------------------------------------[0m-
[1mInput/output options[0m
[0;34minput : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/samplesheet/v3.10/samplesheet_test.csv[0m
[0;34moutdir : [0;32m/home/runner/work/rnaseq/rnaseq/~/tests/908031450a7ded0286feeb8349fa90b1/output[0m
[1mReference genome options[0m
[0;34mfasta : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/genome.fasta[0m
[0;34mgtf : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/genes_with_empty_tid.gtf.gz[0m
[0;34mgff : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/genes.gff.gz[0m
[0;34mtranscript_fasta : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/transcriptome.fasta[0m
[0;34madditional_fasta : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/gfp.fa.gz[0m
[0;34mhisat2_index : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/hisat2.tar.gz[0m
[0;34mrsem_index : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/rsem.tar.gz[0m
[0;34msalmon_index : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/salmon.tar.gz[0m
[0;34mhisat2_build_memory : [0;32m3.GB[0m
[1mRead filtering options[0m
[0;34mbbsplit_fasta_list : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/bbsplit_fasta_list.txt[0m
[1mUMI options[0m
[0;34mumitools_bc_pattern : [0;32mNNNN[0m
[1mAlignment options[0m
[0;34mpseudo_aligner : [0;32msalmon[0m
[1mProcess skipping options[0m
[0;34mskip_bbsplit : [0;32mfalse[0m
[0;34mskip_alignment : [0;32mtrue[0m
[0;34mskip_qc : [0;32mtrue[0m
[1mInstitutional config options[0m
[0;34mconfig_profile_name : [0;32mTest profile[0m
[0;34mconfig_profile_description : [0;32mMinimal test dataset to check pipeline function[0m
[1mGeneric options[0m
[0;34mpipelines_testdata_base_path: [0;32ms3://ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/[0m
[1mCore Nextflow options[0m
[0;34mrunName : [0;32mzen_faraday[0m
[0;34mcontainerEngine : [0;32mdocker[0m
[0;34mlaunchDir : [0;32m/home/runner/work/rnaseq/rnaseq/~/tests/908031450a7ded0286feeb8349fa90b1[0m
[0;34mworkDir : [0;32m/home/runner/work/rnaseq/rnaseq/~/tests/908031450a7ded0286feeb8349fa90b1/work[0m
[0;34mprojectDir : [0;32m/home/runner/work/rnaseq/rnaseq[0m
[0;34muserName : [0;32mrunner[0m
[0;34mprofile : [0;32mtest,docker[0m
[0;34mconfigFiles : [0;32m[0m
!! Only displaying parameters that differ from the pipeline defaults !!
-[2m----------------------------------------------------[0m-
* The pipeline
https://doi.org/10.5281/zenodo.1400710
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
https://github.com/nf-core/rnaseq/blob/master/CITATIONS.md
WARN: The following invalid input values have been detected:
* --modules_testdata_base_path: s3://ngi-igenomes/testdata/nf-core/modules/
WARN: nf-core pipelines do not accept positional arguments. The positional argument `true` has been detected.
HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.
WARN: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Both '--gtf' and '--gff' parameters have been provided.
Using GTF file as priority.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
WARN: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
'--transcript_fasta' parameter has been provided.
Make sure transcript names in this file match those in the GFF/GTF file.
Please see:
https://github.com/nf-core/rnaseq/issues/753
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
WARN: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
'--skip_alignment' parameter has been provided.
Skipping alignment, genome-based quantification and all downstream QC processes.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition
[22/78d6f8] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)
[5a/25dc6a] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes_with_empty_tid.gtf.gz)
[d4/802624] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (RAP1_IAA_30M_REP1)
ERROR ~ Error executing process > 'NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)'
Caused by:
Process `NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)` terminated with an error exit status (126)
Command executed:
touch gfp.fa
cat <<-END_VERSIONS > versions.yml
"NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA":
gunzip: $(echo $(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*$//')
END_VERSIONS
Command exit status:
126
Command output:
(empty)
Command error:
/bin/bash: line 10: .command.run: Permission denied
Work dir:
/home/runner/work/rnaseq/rnaseq/~/tests/908031450a7ded0286feeb8349fa90b1/work/22/78d6f862b9e5b14f0e349a22078af9
Container:
quay.io/nf-core/ubuntu:22.04
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
-- Check '/home/runner/work/rnaseq/rnaseq/~/tests/908031450a7ded0286feeb8349fa90b1/meta/nextflow.log' file for details
Execution cancelled -- Finishing pending tasks before exit
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting
-- Check '/home/runner/work/rnaseq/rnaseq/~/tests/908031450a7ded0286feeb8349fa90b1/meta/nextflow.log' file for details
-[0;35m[nf-core/rnaseq][0;31m Pipeline completed with errors[0m-
Nextflow stderr:
Loading