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drpatelhdrpatelh
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Merge pull request #886 from nf-core/subworkflows-install
nf-core subworkflows install
2 parents fd34718 + 2cf2c96 commit 24eb379

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25 files changed

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‎conf/modules.config‎

Lines changed: 31 additions & 31 deletions
Original file line numberDiff line numberDiff line change
@@ -172,15 +172,15 @@ if (!params.skip_bbsplit && params.bbsplit_fasta_list) {
172172

173173
if (!(params.skip_fastqc || params.skip_qc)) {
174174
process {
175-
withName: '.*:FASTQC_UMITOOLS_TRIMGALORE:FASTQC' {
175+
withName: '.*:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC' {
176176
ext.args = '--quiet'
177177
}
178178
}
179179
}
180180

181181
if (!params.skip_trimming) {
182182
process {
183-
withName: '.*:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE' {
183+
withName: '.*:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE' {
184184
ext.args = {
185185
[
186186
"--fastqc_args '-t ${task.cpus}' ",
@@ -218,7 +218,7 @@ if (!params.skip_trimming) {
218218

219219
if (params.with_umi && !params.skip_umi_extract) {
220220
process {
221-
withName: '.*:FASTQC_UMITOOLS_TRIMGALORE:UMITOOLS_EXTRACT' {
221+
withName: '.*:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:UMITOOLS_EXTRACT' {
222222
ext.args = [
223223
params.umitools_extract_method ? "--extract-method=${params.umitools_extract_method}" : '',
224224
params.umitools_bc_pattern ? "--bc-pattern='${params.umitools_bc_pattern}'" : '',
@@ -293,7 +293,7 @@ if (params.remove_ribo_rna) {
293293

294294
if (!params.skip_alignment) {
295295
process {
296-
withName: 'NFCORE_RNASEQ:RNASEQ:.*:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:.*' {
296+
withName: 'NFCORE_RNASEQ:RNASEQ:.*:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:.*' {
297297
ext.prefix = { "${meta.id}.sorted.bam" }
298298
publishDir = [
299299
path: { "${params.outdir}/${params.aligner}/samtools_stats" },
@@ -302,7 +302,7 @@ if (!params.skip_alignment) {
302302
]
303303
}
304304

305-
withName: 'NFCORE_RNASEQ:RNASEQ:.*:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT' {
305+
withName: 'NFCORE_RNASEQ:RNASEQ:.*:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT' {
306306
ext.prefix = { "${meta.id}.sorted" }
307307
publishDir = [
308308
path: { "${params.outdir}/${params.aligner}" },
@@ -316,7 +316,7 @@ if (!params.skip_alignment) {
316316
]
317317
}
318318

319-
withName: 'NFCORE_RNASEQ:RNASEQ:.*:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX' {
319+
withName: 'NFCORE_RNASEQ:RNASEQ:.*:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX' {
320320
ext.args = params.bam_csi_index ? '-c' : ''
321321
publishDir = [
322322
path: { "${params.outdir}/${params.aligner}" },
@@ -333,7 +333,7 @@ if (!params.skip_alignment) {
333333

334334
if (!params.skip_markduplicates) {
335335
process {
336-
withName: '.*:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES' {
336+
withName: '.*:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES' {
337337
ext.args = '--ASSUME_SORTED true --REMOVE_DUPLICATES false --VALIDATION_STRINGENCY LENIENT --TMP_DIR tmp'
338338
ext.prefix = { "${meta.id}.markdup.sorted" }
339339
publishDir = [
@@ -350,7 +350,7 @@ if (!params.skip_alignment) {
350350
]
351351
}
352352

353-
withName: '.*:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX' {
353+
withName: '.*:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX' {
354354
ext.args = params.bam_csi_index ? '-c' : ''
355355
ext.prefix = { "${meta.id}.markdup.sorted" }
356356
publishDir = [
@@ -360,7 +360,7 @@ if (!params.skip_alignment) {
360360
]
361361
}
362362

363-
withName: '.*:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:.*' {
363+
withName: '.*:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:.*' {
364364
ext.prefix = { "${meta.id}.markdup.sorted.bam" }
365365
publishDir = [
366366
path: { "${params.outdir}/${params.aligner}/samtools_stats" },
@@ -373,7 +373,7 @@ if (!params.skip_alignment) {
373373

374374
if (params.with_umi && ['star_salmon','hisat2'].contains(params.aligner)) {
375375
process {
376-
withName: '.*:DEDUP_UMI_UMITOOLS_GENOME:UMITOOLS_DEDUP' {
376+
withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME:UMITOOLS_DEDUP' {
377377
ext.args = { [
378378
meta.single_end ? '' : '--unpaired-reads=discard --chimeric-pairs=discard',
379379
params.umitools_grouping_method ? "--method='${params.umitools_grouping_method}'" : '',
@@ -399,7 +399,7 @@ if (!params.skip_alignment) {
399399
]
400400
}
401401

402-
withName: '.*:DEDUP_UMI_UMITOOLS_GENOME:SAMTOOLS_INDEX' {
402+
withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME:SAMTOOLS_INDEX' {
403403
ext.args = params.bam_csi_index ? '-c' : ''
404404
ext.prefix = { "${meta.id}.umi_dedup.sorted" }
405405
publishDir = [
@@ -414,7 +414,7 @@ if (!params.skip_alignment) {
414414
]
415415
}
416416

417-
withName: '.*:DEDUP_UMI_UMITOOLS_GENOME:BAM_STATS_SAMTOOLS:.*' {
417+
withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME:BAM_STATS_SAMTOOLS:.*' {
418418
ext.prefix = { "${meta.id}.umi_dedup.sorted.bam" }
419419
publishDir = [
420420
path: { "${params.outdir}/${params.aligner}/samtools_stats" },
@@ -435,15 +435,15 @@ if (!params.skip_alignment) {
435435
]
436436
}
437437

438-
withName: '.*:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP' {
438+
withName: '.*:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP' {
439439
ext.prefix = { "${meta.id}.clip.forward" }
440440
publishDir = [
441441
path: { "${params.outdir}/${params.aligner}" },
442442
enabled: false
443443
]
444444
}
445445

446-
withName: '.*:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG' {
446+
withName: '.*:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG' {
447447
ext.prefix = { "${meta.id}.forward" }
448448
publishDir = [
449449
path: { "${params.outdir}/${params.aligner}/bigwig" },
@@ -452,15 +452,15 @@ if (!params.skip_alignment) {
452452
]
453453
}
454454

455-
withName: '.*:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP' {
455+
withName: '.*:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP' {
456456
ext.prefix = { "${meta.id}.clip.reverse" }
457457
publishDir = [
458458
path: { "${params.outdir}/${params.aligner}" },
459459
enabled: false
460460
]
461461
}
462462

463-
withName: '.*:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG' {
463+
withName: '.*:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG' {
464464
ext.prefix = { "${meta.id}.reverse" }
465465
publishDir = [
466466
path: { "${params.outdir}/${params.aligner}/bigwig" },
@@ -593,30 +593,30 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') {
593593
]
594594
}
595595

596-
withName: 'NFCORE_RNASEQ:RNASEQ:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT' {
596+
withName: 'NFCORE_RNASEQ:RNASEQ:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT' {
597597
ext.prefix = { "${meta.id}.transcriptome.sorted" }
598598
publishDir = [
599599
path: { "${params.outdir}/${params.aligner}" },
600600
enabled: false
601601
]
602602
}
603603

604-
withName: 'NFCORE_RNASEQ:RNASEQ:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX' {
604+
withName: 'NFCORE_RNASEQ:RNASEQ:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX' {
605605
publishDir = [
606606
path: { "${params.outdir}/${params.aligner}" },
607607
enabled: false
608608
]
609609
}
610610

611-
withName: 'NFCORE_RNASEQ:RNASEQ:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:.*' {
611+
withName: 'NFCORE_RNASEQ:RNASEQ:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:.*' {
612612
ext.prefix = { "${meta.id}.transcriptome.sorted.bam" }
613613
publishDir = [
614614
path: { "${params.outdir}/${params.aligner}" },
615615
enabled: false
616616
]
617617
}
618618

619-
withName: '.*:DEDUP_UMI_UMITOOLS_TRANSCRIPTOME:UMITOOLS_DEDUP' {
619+
withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME:UMITOOLS_DEDUP' {
620620
ext.args = { [
621621
meta.single_end ? '' : '--unpaired-reads=discard --chimeric-pairs=discard',
622622
params.umitools_grouping_method ? "--method='${params.umitools_grouping_method}'" : '',
@@ -630,14 +630,14 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') {
630630
]
631631
}
632632

633-
withName: '.*:DEDUP_UMI_UMITOOLS_TRANSCRIPTOME:SAMTOOLS_INDEX' {
633+
withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME:SAMTOOLS_INDEX' {
634634
publishDir = [
635635
path: { "${params.outdir}/${params.aligner}" },
636636
enabled: false
637637
]
638638
}
639639

640-
withName: '.*:DEDUP_UMI_UMITOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:.*' {
640+
withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:.*' {
641641
ext.prefix = { "${meta.id}.umi_dedup.transcriptome.sorted.bam" }
642642
publishDir = [
643643
path: { "${params.outdir}/${params.aligner}/samtools_stats" },
@@ -739,7 +739,7 @@ if (!params.skip_alignment && params.aligner == 'star_rsem') {
739739

740740
if (!params.skip_alignment && params.aligner == 'hisat2') {
741741
process {
742-
withName: '.*:ALIGN_HISAT2:HISAT2_ALIGN' {
742+
withName: '.*:FASTQ_ALIGN_HISAT2:HISAT2_ALIGN' {
743743
ext.args = '--met-stderr --new-summary --dta'
744744
publishDir = [
745745
[
@@ -862,7 +862,7 @@ if (!params.skip_alignment && !params.skip_qc) {
862862

863863
if (!params.skip_rseqc && 'bam_stat' in rseqc_modules) {
864864
process {
865-
withName: '.*:RSEQC:RSEQC_BAMSTAT' {
865+
withName: '.*:BAM_RSEQC:RSEQC_BAMSTAT' {
866866
publishDir = [
867867
path: { "${params.outdir}/${params.aligner}/rseqc/bam_stat" },
868868
mode: params.publish_dir_mode,
@@ -874,7 +874,7 @@ if (!params.skip_alignment && !params.skip_qc) {
874874

875875
if (!params.skip_rseqc && 'infer_experiment' in rseqc_modules) {
876876
process {
877-
withName: '.*:RSEQC:RSEQC_INFEREXPERIMENT' {
877+
withName: '.*:BAM_RSEQC:RSEQC_INFEREXPERIMENT' {
878878
publishDir = [
879879
path: { "${params.outdir}/${params.aligner}/rseqc/infer_experiment" },
880880
mode: params.publish_dir_mode,
@@ -886,7 +886,7 @@ if (!params.skip_alignment && !params.skip_qc) {
886886

887887
if (!params.skip_rseqc && 'junction_annotation' in rseqc_modules) {
888888
process {
889-
withName: '.*:RSEQC:RSEQC_JUNCTIONANNOTATION' {
889+
withName: '.*:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION' {
890890
publishDir = [
891891
[
892892
path: { "${params.outdir}/${params.aligner}/rseqc/junction_annotation/pdf" },
@@ -920,7 +920,7 @@ if (!params.skip_alignment && !params.skip_qc) {
920920

921921
if (!params.skip_rseqc && 'junction_saturation' in rseqc_modules) {
922922
process {
923-
withName: '.*:RSEQC:RSEQC_JUNCTIONSATURATION' {
923+
withName: '.*:BAM_RSEQC:RSEQC_JUNCTIONSATURATION' {
924924
publishDir = [
925925
[
926926
path: { "${params.outdir}/${params.aligner}/rseqc/junction_saturation/pdf" },
@@ -939,7 +939,7 @@ if (!params.skip_alignment && !params.skip_qc) {
939939

940940
if (!params.skip_rseqc && 'read_duplication' in rseqc_modules) {
941941
process {
942-
withName: '.*:RSEQC:RSEQC_READDUPLICATION' {
942+
withName: '.*:BAM_RSEQC:RSEQC_READDUPLICATION' {
943943
publishDir = [
944944
[
945945
path: { "${params.outdir}/${params.aligner}/rseqc/read_duplication/pdf" },
@@ -963,7 +963,7 @@ if (!params.skip_alignment && !params.skip_qc) {
963963

964964
if (!params.skip_rseqc && 'read_distribution' in rseqc_modules && !params.bam_csi_index) {
965965
process {
966-
withName: '.*:RSEQC:RSEQC_READDISTRIBUTION' {
966+
withName: '.*:BAM_RSEQC:RSEQC_READDISTRIBUTION' {
967967
publishDir = [
968968
path: { "${params.outdir}/${params.aligner}/rseqc/read_distribution" },
969969
mode: params.publish_dir_mode,
@@ -975,7 +975,7 @@ if (!params.skip_alignment && !params.skip_qc) {
975975

976976
if (!params.skip_rseqc && 'inner_distance' in rseqc_modules && !params.bam_csi_index) {
977977
process {
978-
withName: '.*:RSEQC:RSEQC_INNERDISTANCE' {
978+
withName: '.*:BAM_RSEQC:RSEQC_INNERDISTANCE' {
979979
publishDir = [
980980
[
981981
path: { "${params.outdir}/${params.aligner}/rseqc/inner_distance/txt" },
@@ -1000,7 +1000,7 @@ if (!params.skip_alignment && !params.skip_qc) {
10001000

10011001
if (!params.skip_rseqc && 'tin' in rseqc_modules && !params.bam_csi_index) {
10021002
process {
1003-
withName: '.*:RSEQC:RSEQC_TIN' {
1003+
withName: '.*:BAM_RSEQC:RSEQC_TIN' {
10041004
publishDir = [
10051005
path: { "${params.outdir}/${params.aligner}/rseqc/tin" },
10061006
mode: params.publish_dir_mode,

‎modules.json‎

Lines changed: 38 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -48,7 +48,7 @@
4848
},
4949
"picard/markduplicates": {
5050
"branch": "master",
51-
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
51+
"git_sha": "eca65aa4a5e2e192ac44d6962c8f9260f314ffb8"
5252
},
5353
"preseq/lcextrap": {
5454
"branch": "master",
@@ -148,7 +148,7 @@
148148
},
149149
"trimgalore": {
150150
"branch": "master",
151-
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
151+
"git_sha": "b51a69e30973c71950225c817ad07a3337d22c40"
152152
},
153153
"ucsc/bedclip": {
154154
"branch": "master",
@@ -171,6 +171,42 @@
171171
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
172172
}
173173
}
174+
},
175+
"subworkflows": {
176+
"nf-core": {
177+
"bam_dedup_stats_samtools_umitools": {
178+
"branch": "master",
179+
"git_sha": "41891ec2c3704911cd68b9317f26545b95a1c48d"
180+
},
181+
"bam_markduplicates_picard": {
182+
"branch": "master",
183+
"git_sha": "c9083a16a9a6c5e5beea40a88939b6e1138926f7"
184+
},
185+
"bam_rseqc": {
186+
"branch": "master",
187+
"git_sha": "36a77f7c6decf2d1fb9f639ae982bc148d6828aa"
188+
},
189+
"bam_sort_stats_samtools": {
190+
"branch": "master",
191+
"git_sha": "3911652a6b24249358f79e8b8466338d63efb2a2"
192+
},
193+
"bam_stats_samtools": {
194+
"branch": "master",
195+
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
196+
},
197+
"bedgraph_bedclip_bedgraphtobigwig": {
198+
"branch": "master",
199+
"git_sha": "b81a313d8fac0a82a8a4ff0de80590b2f97f11ad"
200+
},
201+
"fastq_align_hisat2": {
202+
"branch": "master",
203+
"git_sha": "9057e75e8ac959373a72a9402130fdea2e2d1398"
204+
},
205+
"fastq_fastqc_umitools_trimgalore": {
206+
"branch": "master",
207+
"git_sha": "b51a69e30973c71950225c817ad07a3337d22c40"
208+
}
209+
}
174210
}
175211
}
176212
}

‎modules/nf-core/picard/markduplicates/main.nf‎

Lines changed: 3 additions & 0 deletions
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‎modules/nf-core/picard/markduplicates/meta.yml‎

Lines changed: 9 additions & 1 deletion
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