Use module config

Signed-off-by: Ben Sherman <[email protected]>

main.nf

@@ -59,7 +59,7 @@ WorkflowMain.initialise(workflow, params, log)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { RNASEQ } from './workflows/rnaseq'
+include { RNASEQ } from './workflows/rnaseq/main'
 
 //
 // WORKFLOW: Run main nf-core/rnaseq analysis pipeline

subworkflows/local/align_star/module.config

@@ -0,0 +1,36 @@
+
+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',
+            saveAs: { params.save_align_intermeds ? it : null }
+        ],
+        [
+            path: { "${params.outdir}/${params.aligner}/unmapped" },
+            mode: params.publish_dir_mode,
+            pattern: '*.fastq.gz',
+            saveAs: { params.save_unaligned ? it : null }
+        ]
+    ]
+}

subworkflows/local/prepare_genome/module.config

@@ -0,0 +1,96 @@
+
+withName: 'GUNZIP_.*|MAKE_TRANSCRIPTS_FASTA' {
+    publishDir = [
+        path: { "${params.outdir}/genome" },
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
+    ]
+}
+
+withName: 'UNTAR_.*' {
+    ext.args2 = '--no-same-owner'
+}
+
+withName: 'UNTAR_.*|STAR_GENOMEGENERATE|STAR_GENOMEGENERATE_IGENOMES|HISAT2_BUILD' {
+    publishDir = [
+        path: { "${params.outdir}/genome/index" },
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
+    ]
+}
+
+withName: 'GFFREAD' {
+    ext.args   = '--keep-exon-attrs -F -T'
+    publishDir = [
+        path: { "${params.outdir}/genome" },
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
+    ]
+}
+
+withName: 'HISAT2_EXTRACTSPLICESITES' {
+    publishDir = [
+        path: { "${params.outdir}/genome/index" },
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
+    ]
+}
+
+withName: 'SALMON_INDEX' {
+    ext.args   = params.gencode ? '--gencode' : ''
+    publishDir = [
+        path: { "${params.outdir}/genome/index" },
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
+    ]
+}
+
+withName: 'RSEM_PREPAREREFERENCE_GENOME' {
+    ext.args   = '--star'
+    publishDir = [
+        path: { "${params.outdir}/genome/index" },
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
+    ]
+}
+
+withName: 'GTF2BED' {
+    publishDir = [
+        path: { "${params.outdir}/genome" },
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
+    ]
+}
+
+withName: 'CAT_ADDITIONAL_FASTA|PREPROCESS_TRANSCRIPTS_FASTA_GENCODE' {
+    publishDir = [
+        path: { "${params.outdir}/genome" },
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
+    ]
+}
+
+withName: 'GTF_GENE_FILTER' {
+    publishDir = [
+        path: { "${params.outdir}/genome" },
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
+    ]
+}
+
+withName: 'CUSTOM_GETCHROMSIZES' {
+    publishDir = [
+        path: { "${params.outdir}/genome" },
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
+    ]
+}
+
+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 : params.save_reference ? filename : null }
+    ]
+}

subworkflows/local/quantify_rsem/module.config

@@ -0,0 +1,36 @@
+
+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",
+            saveAs: { params.save_align_intermeds ? it : null }
+        ],
+        [
+            path: { "${params.outdir}/${params.aligner}/log" },
+            mode: params.publish_dir_mode,
+            pattern: "*.log"
+        ]
+    ]
+}
+
+withName: 'RSEM_MERGE_COUNTS' {
+    publishDir = [
+        path: { "${params.outdir}/${params.aligner}" },
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+    ]
+}

subworkflows/local/quantify_salmon/module.config

@@ -0,0 +1,33 @@
+
+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 }
+    ]
+}
+
+withName: 'SALMON_TX2GENE' {
+    publishDir = [
+        path: { "${params.outdir}/${params.pseudo_aligner}" },
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+    ]
+}
+
+withName: 'SALMON_TXIMPORT' {
+    publishDir = [
+        path: { "${params.outdir}/${params.pseudo_aligner}" },
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+    ]
+}
+
+withName: 'SALMON_SE_.*' {
+    publishDir = [
+        path: { "${params.outdir}/${params.pseudo_aligner}" },
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+    ]
+}