-
Notifications
You must be signed in to change notification settings - Fork 118
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge remote-tracking branch 'upstream/dev' into dev-checkm2
- Loading branch information
Showing
3 changed files
with
192 additions
and
174 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,178 @@ | ||
| /* | ||
| * SHORTREAD_PREPROCESSING: Preprocessing and QC for short reads | ||
| */ | ||
|
|
||
| include { FASTQC as FASTQC_RAW } from '../../modules/nf-core/fastqc/main' | ||
| include { FASTQC as FASTQC_TRIMMED } from '../../modules/nf-core/fastqc/main' | ||
| include { FASTP } from '../../modules/nf-core/fastp/main' | ||
| include { ADAPTERREMOVAL as ADAPTERREMOVAL_PE } from '../../modules/nf-core/adapterremoval/main' | ||
| include { ADAPTERREMOVAL as ADAPTERREMOVAL_SE } from '../../modules/nf-core/adapterremoval/main' | ||
| include { BOWTIE2_REMOVAL_BUILD as BOWTIE2_HOST_REMOVAL_BUILD } from '../../modules/local/bowtie2_removal_build' | ||
| include { BOWTIE2_REMOVAL_ALIGN as BOWTIE2_HOST_REMOVAL_ALIGN } from '../../modules/local/bowtie2_removal_align' | ||
| include { BOWTIE2_REMOVAL_BUILD as BOWTIE2_PHIX_REMOVAL_BUILD } from '../../modules/local/bowtie2_removal_build' | ||
| include { BOWTIE2_REMOVAL_ALIGN as BOWTIE2_PHIX_REMOVAL_ALIGN } from '../../modules/local/bowtie2_removal_align' | ||
| include { CAT_FASTQ } from '../../modules/nf-core/cat/fastq/main' | ||
| include { SEQTK_MERGEPE } from '../../modules/nf-core/seqtk/mergepe/main' | ||
| include { BBMAP_BBNORM } from '../../modules/nf-core/bbmap/bbnorm/main' | ||
|
|
||
| workflow SHORTREAD_PREPROCESSING { | ||
| take: | ||
| ch_raw_short_reads // [ [meta] , fastq1, fastq2] (mandatory) | ||
| ch_host_fasta // [fasta] (optional) | ||
| ch_phix_db_file // [fasta] (optional) | ||
| ch_metaeuk_db // [fasta] (optional) | ||
|
|
||
| main: | ||
| ch_versions = Channel.empty() | ||
| ch_multiqc_files = Channel.empty() | ||
|
|
||
| FASTQC_RAW( | ||
| ch_raw_short_reads | ||
| ) | ||
| ch_versions = ch_versions.mix(FASTQC_RAW.out.versions.first()) | ||
| ch_multiqc_files = ch_multiqc_files.mix(FASTQC_RAW.out.zip) | ||
|
|
||
| if (!params.skip_clipping) { | ||
| if (params.clip_tool == 'fastp') { | ||
| FASTP( | ||
| ch_raw_short_reads, | ||
| [], | ||
| params.fastp_save_trimmed_fail, | ||
| [] | ||
| ) | ||
| ch_short_reads_prepped = FASTP.out.reads | ||
| ch_versions = ch_versions.mix(FASTP.out.versions.first()) | ||
| ch_multiqc_files = ch_multiqc_files.mix(FASTP.out.json) | ||
|
|
||
| } | ||
| else if (params.clip_tool == 'adapterremoval') { | ||
|
|
||
| // due to strange output file scheme in AR2, have to manually separate | ||
| // SE/PE to allow correct pulling of reads after. | ||
| ch_adapterremoval_in = ch_raw_short_reads.branch { | ||
| single: it[0]['single_end'] | ||
| paired: !it[0]['single_end'] | ||
| } | ||
|
|
||
| ADAPTERREMOVAL_PE(ch_adapterremoval_in.paired, []) | ||
| ADAPTERREMOVAL_SE(ch_adapterremoval_in.single, []) | ||
|
|
||
| ch_short_reads_prepped = Channel.empty() | ||
| ch_short_reads_prepped = ch_short_reads_prepped.mix(ADAPTERREMOVAL_SE.out.singles_truncated, ADAPTERREMOVAL_PE.out.paired_truncated) | ||
|
|
||
| ch_versions = ch_versions.mix(ADAPTERREMOVAL_PE.out.versions.first(), ADAPTERREMOVAL_SE.out.versions.first()) | ||
| ch_multiqc_files = ch_multiqc_files.mix(ADAPTERREMOVAL_PE.out.settings) | ||
| ch_multiqc_files = ch_multiqc_files.mix(ADAPTERREMOVAL_SE.out.settings) | ||
| } | ||
| } | ||
| else { | ||
| ch_short_reads_prepped = ch_raw_short_reads | ||
| } | ||
|
|
||
| if (params.host_fasta) { | ||
| if (params.host_fasta_bowtie2index) { | ||
| ch_host_bowtie2index = file(params.host_fasta_bowtie2index, checkIfExists: true) | ||
| } | ||
| else { | ||
| BOWTIE2_HOST_REMOVAL_BUILD( | ||
| ch_host_fasta | ||
| ) | ||
| ch_host_bowtie2index = BOWTIE2_HOST_REMOVAL_BUILD.out.index | ||
| } | ||
| } | ||
|
|
||
| if (params.host_fasta || params.host_genome) { | ||
| BOWTIE2_HOST_REMOVAL_ALIGN( | ||
| ch_short_reads_prepped, | ||
| ch_host_bowtie2index | ||
| ) | ||
| ch_short_reads_hostremoved = BOWTIE2_HOST_REMOVAL_ALIGN.out.reads | ||
| ch_versions = ch_versions.mix(BOWTIE2_HOST_REMOVAL_ALIGN.out.versions.first()) | ||
| ch_multiqc_files = ch_multiqc_files.mix(BOWTIE2_HOST_REMOVAL_ALIGN.out.log) | ||
| } | ||
| else { | ||
| ch_short_reads_hostremoved = ch_short_reads_prepped | ||
| } | ||
|
|
||
| if (!params.keep_phix) { | ||
| BOWTIE2_PHIX_REMOVAL_BUILD( | ||
| ch_phix_db_file | ||
| ) | ||
| BOWTIE2_PHIX_REMOVAL_ALIGN( | ||
| ch_short_reads_hostremoved, | ||
| BOWTIE2_PHIX_REMOVAL_BUILD.out.index | ||
| ) | ||
| ch_short_reads_phixremoved = BOWTIE2_PHIX_REMOVAL_ALIGN.out.reads | ||
| ch_versions = ch_versions.mix(BOWTIE2_PHIX_REMOVAL_ALIGN.out.versions.first()) | ||
| ch_multiqc_files = ch_multiqc_files.mix(BOWTIE2_PHIX_REMOVAL_ALIGN.out.log) | ||
| } | ||
| else { | ||
| ch_short_reads_phixremoved = ch_short_reads_hostremoved | ||
| } | ||
|
|
||
| if (!(params.keep_phix && params.skip_clipping && !(params.host_genome || params.host_fasta))) { | ||
| FASTQC_TRIMMED( | ||
| ch_short_reads_phixremoved | ||
| ) | ||
| ch_versions = ch_versions.mix(FASTQC_TRIMMED.out.versions) | ||
| ch_multiqc_files = ch_multiqc_files.mix(FASTQC_TRIMMED.out.zip) | ||
| } | ||
|
|
||
| // Run/Lane merging | ||
|
|
||
| ch_short_reads_forcat = ch_short_reads_phixremoved | ||
| .map { meta, reads -> | ||
| def meta_new = meta - meta.subMap('run') | ||
| [meta_new, reads] | ||
| } | ||
| .groupTuple() | ||
| .branch { meta, reads -> | ||
| cat: reads.size() >= 2 | ||
| skip_cat: true | ||
| } | ||
|
|
||
| CAT_FASTQ(ch_short_reads_forcat.cat.map { meta, reads -> [meta, reads.flatten()] }) | ||
|
|
||
| // Ensure we don't have nests of nests so that structure is in form expected for assembly | ||
| ch_short_reads_catskipped = ch_short_reads_forcat.skip_cat.map { meta, reads -> | ||
| def new_reads = meta.single_end ? reads[0] : reads.flatten() | ||
| [meta, new_reads] | ||
| } | ||
|
|
||
| // Combine single run and multi-run-merged data | ||
| ch_short_reads = Channel.empty() | ||
| ch_short_reads = CAT_FASTQ.out.reads.mix(ch_short_reads_catskipped) | ||
| ch_versions = ch_versions.mix(CAT_FASTQ.out.versions.first()) | ||
|
|
||
| if (params.bbnorm) { | ||
| if (params.coassemble_group) { | ||
| // Interleave pairs, to be able to treat them as single ends when calling bbnorm. This prepares | ||
| // for dropping the single_end parameter, but keeps assembly modules as they are, i.e. not | ||
| // accepting a mix of single end and pairs. | ||
| SEQTK_MERGEPE( | ||
| ch_short_reads.filter { !it[0].single_end } | ||
| ) | ||
| ch_versions = ch_versions.mix(SEQTK_MERGEPE.out.versions.first()) | ||
| // Combine the interleaved pairs with any single end libraries. Set the meta.single_end to true (used by the bbnorm module). | ||
| ch_bbnorm = SEQTK_MERGEPE.out.reads | ||
| .mix(ch_short_reads.filter { it[0].single_end }) | ||
| .map { [[id: sprintf("group%s", it[0].group), group: it[0].group, single_end: true], it[1]] } | ||
| .groupTuple() | ||
| } | ||
| else { | ||
| ch_bbnorm = ch_short_reads | ||
| } | ||
| BBMAP_BBNORM(ch_bbnorm) | ||
| ch_versions = ch_versions.mix(BBMAP_BBNORM.out.versions) | ||
| ch_short_reads_assembly = BBMAP_BBNORM.out.fastq | ||
| } | ||
| else { | ||
| ch_short_reads_assembly = ch_short_reads | ||
| } | ||
|
|
||
| emit: | ||
| short_reads = ch_short_reads | ||
| short_reads_assembly = ch_short_reads_assembly | ||
| versions = ch_versions | ||
| multiqc_files = ch_multiqc_files | ||
| } |
Oops, something went wrong.