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Signed-off-by: Ben Sherman <[email protected]>
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,36 @@ | ||
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| withName: 'STAR_ALIGN|STAR_ALIGN_IGENOMES' { | ||
| ext.args = [ | ||
| '--quantMode TranscriptomeSAM', | ||
| '--twopassMode Basic', | ||
| '--outSAMtype BAM Unsorted', | ||
| '--readFilesCommand zcat', | ||
| '--runRNGseed 0', | ||
| '--outFilterMultimapNmax 20', | ||
| '--alignSJDBoverhangMin 1', | ||
| '--outSAMattributes NH HI AS NM MD', | ||
| '--quantTranscriptomeBan Singleend', | ||
| '--outSAMstrandField intronMotif', | ||
| params.save_unaligned ? '--outReadsUnmapped Fastx' : '', | ||
| params.extra_star_align_args ? params.extra_star_align_args.split("\\s(?=--)") : '' | ||
| ].flatten().unique(false).join(' ').trim() | ||
| publishDir = [ | ||
| [ | ||
| path: "${params.outdir}/${params.aligner}/log", | ||
| mode: params.publish_dir_mode, | ||
| pattern: '*.{out,tab}' | ||
| ], | ||
| [ | ||
| path: "${params.outdir}/${params.aligner}", | ||
| mode: params.publish_dir_mode, | ||
| pattern: '*.bam', | ||
| enabled: params.save_align_intermeds | ||
| ], | ||
| [ | ||
| path: "${params.outdir}/${params.aligner}/unmapped", | ||
| mode: params.publish_dir_mode, | ||
| pattern: '*.fastq.gz', | ||
| enabled: params.save_unaligned | ||
| ] | ||
| ] | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,8 @@ | ||
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| withName: 'SAMPLESHEET_CHECK' { | ||
| publishDir = [ | ||
| path: "${params.outdir}/pipeline_info", | ||
| mode: params.publish_dir_mode, | ||
| saveAs: { filename -> filename.equals('versions.yml') ? null : filename } | ||
| ] | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,107 @@ | ||
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| withName: 'GUNZIP_.*|MAKE_TRANSCRIPTS_FASTA' { | ||
| publishDir = [ | ||
| path: "${params.outdir}/genome", | ||
| mode: params.publish_dir_mode, | ||
| saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, | ||
| enabled: params.save_reference | ||
| ] | ||
| } | ||
|
|
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| withName: 'UNTAR_.*' { | ||
| ext.args2 = '--no-same-owner' | ||
| } | ||
|
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| withName: 'UNTAR_.*|STAR_GENOMEGENERATE|STAR_GENOMEGENERATE_IGENOMES|HISAT2_BUILD' { | ||
| publishDir = [ | ||
| path: "${params.outdir}/genome/index", | ||
| mode: params.publish_dir_mode, | ||
| saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, | ||
| enabled: params.save_reference | ||
| ] | ||
| } | ||
|
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| withName: 'GFFREAD' { | ||
| ext.args = '--keep-exon-attrs -F -T' | ||
| publishDir = [ | ||
| path: "${params.outdir}/genome", | ||
| mode: params.publish_dir_mode, | ||
| saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, | ||
| enabled: params.save_reference | ||
| ] | ||
| } | ||
|
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| withName: 'HISAT2_EXTRACTSPLICESITES' { | ||
| publishDir = [ | ||
| path: "${params.outdir}/genome/index", | ||
| mode: params.publish_dir_mode, | ||
| saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, | ||
| enabled: params.save_reference | ||
| ] | ||
| } | ||
|
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| withName: 'SALMON_INDEX' { | ||
| ext.args = params.gencode ? '--gencode' : '' | ||
| publishDir = [ | ||
| path: "${params.outdir}/genome/index", | ||
| mode: params.publish_dir_mode, | ||
| saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, | ||
| enabled: params.save_reference | ||
| ] | ||
| } | ||
|
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| withName: 'RSEM_PREPAREREFERENCE_GENOME' { | ||
| ext.args = '--star' | ||
| publishDir = [ | ||
| path: "${params.outdir}/genome/index", | ||
| mode: params.publish_dir_mode, | ||
| saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, | ||
| enabled: params.save_reference | ||
| ] | ||
| } | ||
|
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| withName: 'GTF2BED' { | ||
| publishDir = [ | ||
| path: "${params.outdir}/genome", | ||
| mode: params.publish_dir_mode, | ||
| saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, | ||
| enabled: params.save_reference | ||
| ] | ||
| } | ||
|
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| withName: 'CAT_ADDITIONAL_FASTA|PREPROCESS_TRANSCRIPTS_FASTA_GENCODE' { | ||
| publishDir = [ | ||
| path: "${params.outdir}/genome", | ||
| mode: params.publish_dir_mode, | ||
| saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, | ||
| enabled: params.save_reference | ||
| ] | ||
| } | ||
|
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| withName: 'GTF_GENE_FILTER' { | ||
| publishDir = [ | ||
| path: "${params.outdir}/genome", | ||
| mode: params.publish_dir_mode, | ||
| saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, | ||
| enabled: params.save_reference | ||
| ] | ||
| } | ||
|
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| withName: 'CUSTOM_GETCHROMSIZES' { | ||
| publishDir = [ | ||
| path: "${params.outdir}/genome", | ||
| mode: params.publish_dir_mode, | ||
| saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, | ||
| enabled: params.save_reference | ||
| ] | ||
| } | ||
|
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| withName: 'BBMAP_BBSPLIT' { | ||
| ext.args = 'build=1' | ||
| publishDir = [ | ||
| path: "${params.outdir}/genome/index", | ||
| mode: params.publish_dir_mode, | ||
| saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, | ||
| enabled: params.save_reference | ||
| ] | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,36 @@ | ||
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| withName: 'RSEM_CALCULATEEXPRESSION' { | ||
| ext.args = [ | ||
| '--star', | ||
| '--star-output-genome-bam', | ||
| '--star-gzipped-read-file', | ||
| '--estimate-rspd', | ||
| '--seed 1' | ||
| ].join(' ').trim() | ||
| publishDir = [ | ||
| [ | ||
| path: "${params.outdir}/${params.aligner}", | ||
| mode: params.publish_dir_mode, | ||
| pattern: "*.{stat,results}" | ||
| ], | ||
| [ | ||
| path: "${params.outdir}/${params.aligner}", | ||
| mode: params.publish_dir_mode, | ||
| pattern: "*.bam", | ||
| enabled: params.save_align_intermeds | ||
| ], | ||
| [ | ||
| path: "${params.outdir}/${params.aligner}/log", | ||
| mode: params.publish_dir_mode, | ||
| pattern: "*.log" | ||
| ] | ||
| ] | ||
| } | ||
|
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| withName: 'RSEM_MERGE_COUNTS' { | ||
| publishDir = [ | ||
| path: "${params.outdir}/${params.aligner}", | ||
| mode: params.publish_dir_mode, | ||
| saveAs: { filename -> filename.equals('versions.yml') ? null : filename } | ||
| ] | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,33 @@ | ||
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| withName: 'SALMON_QUANT' { | ||
| ext.args = params.extra_salmon_quant_args ?: '' | ||
| publishDir = [ | ||
| path: "${params.outdir}/${params.pseudo_aligner}", | ||
| mode: params.publish_dir_mode, | ||
| saveAs: { filename -> filename.equals('versions.yml') || filename.endsWith('_meta_info.json') ? null : filename } | ||
| ] | ||
| } | ||
|
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| withName: 'SALMON_TX2GENE' { | ||
| publishDir = [ | ||
| path: "${params.outdir}/${params.pseudo_aligner}", | ||
| mode: params.publish_dir_mode, | ||
| saveAs: { filename -> filename.equals('versions.yml') ? null : filename } | ||
| ] | ||
| } | ||
|
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| withName: 'SALMON_TXIMPORT' { | ||
| publishDir = [ | ||
| path: "${params.outdir}/${params.pseudo_aligner}", | ||
| mode: params.publish_dir_mode, | ||
| saveAs: { filename -> filename.equals('versions.yml') ? null : filename } | ||
| ] | ||
| } | ||
|
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| withName: 'SALMON_SE_.*' { | ||
| publishDir = [ | ||
| path: "${params.outdir}/${params.pseudo_aligner}", | ||
| mode: params.publish_dir_mode, | ||
| saveAs: { filename -> filename.equals('versions.yml') ? null : filename } | ||
| ] | ||
| } |
36 changes: 36 additions & 0 deletions
36
subworkflows/nf-core/bam_markduplicates_picard/module.config
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