🚚 move nf-core subworflows to local workflows

cnr-ibba · Mar 21, 2024 · 82e4f68 · 82e4f68
1 parent 4836ca0
commit 82e4f68
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Showing 15 changed files with 102 additions and 80 deletions.
diff --git a/modules.json b/modules.json
@@ -70,13 +70,13 @@
           "picard/markduplicates": {
             "branch": "master",
             "git_sha": "20b0918591d4ba20047d7e13e5094bcceba81447",
-            "installed_by": ["bam_markduplicates_picard"],
+            "installed_by": ["modules"],
             "patch": "modules/nf-core/picard/markduplicates/picard-markduplicates.diff"
           },
           "samtools/coverage": {
             "branch": "master",
             "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
-            "installed_by": ["bam_stats_samtools"]
+            "installed_by": ["modules"]
           },
           "samtools/depth": {
             "branch": "master",
@@ -92,22 +92,22 @@
           "samtools/flagstat": {
             "branch": "master",
             "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
-            "installed_by": ["bam_stats_samtools"]
+            "installed_by": ["modules"]
           },
           "samtools/idxstats": {
             "branch": "master",
             "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
-            "installed_by": ["bam_stats_samtools"]
+            "installed_by": ["modules"]
           },
           "samtools/index": {
             "branch": "master",
             "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
-            "installed_by": ["bam_markduplicates_picard"]
+            "installed_by": ["modules"]
           },
           "samtools/stats": {
             "branch": "master",
             "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
-            "installed_by": ["bam_stats_samtools"]
+            "installed_by": ["modules"]
           },
           "tabix/bgzip": {
             "branch": "master",
@@ -125,20 +125,6 @@
             "installed_by": ["modules"]
           }
         }
-      },
-      "subworkflows": {
-        "nf-core": {
-          "bam_markduplicates_picard": {
-            "branch": "master",
-            "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
-            "installed_by": ["subworkflows"]
-          },
-          "bam_stats_samtools": {
-            "branch": "master",
-            "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
-            "installed_by": ["bam_markduplicates_picard"]
-          }
-        }
       }
     }
   }

diff --git a/...nf-core/bam_markduplicates_picard/main.nf → .../local/cram_markduplicates_picard/main.nf b/...nf-core/bam_markduplicates_picard/main.nf → .../local/cram_markduplicates_picard/main.nf
@@ -4,9 +4,9 @@
 
 include { PICARD_MARKDUPLICATES } from '../../../modules/nf-core/picard/markduplicates/main'
 include { SAMTOOLS_INDEX        } from '../../../modules/nf-core/samtools/index/main'
-include { BAM_STATS_SAMTOOLS    } from '../bam_stats_samtools/main'
+include { CRAM_STATS_SAMTOOLS    } from '../cram_stats_samtools/main'
 
-workflow BAM_MARKDUPLICATES_PICARD {
+workflow CRAM_MARKDUPLICATES_PICARD {
 
     take:
     ch_cram  // channel: [ val(meta), path(cram) ]
@@ -31,19 +31,19 @@ workflow BAM_MARKDUPLICATES_PICARD {
             else [ meta, cram, csi ]
         }
 
-    BAM_STATS_SAMTOOLS ( ch_cram_crai, ch_fasta )
-    ch_versions = ch_versions.mix(BAM_STATS_SAMTOOLS.out.versions)
+    CRAM_STATS_SAMTOOLS ( ch_cram_crai, ch_fasta )
+    ch_versions = ch_versions.mix(CRAM_STATS_SAMTOOLS.out.versions)
 
     emit:
     cram     = PICARD_MARKDUPLICATES.out.cram    // channel: [ val(meta), path(cram) ]
     metrics  = PICARD_MARKDUPLICATES.out.metrics // channel: [ val(meta), path(cram) ]
-    crai      = SAMTOOLS_INDEX.out.crai          // channel: [ val(meta), path(crai) ]
+    crai     = SAMTOOLS_INDEX.out.crai          // channel: [ val(meta), path(crai) ]
     csi      = SAMTOOLS_INDEX.out.csi            // channel: [ val(meta), path(csi) ]
 
-    stats    = BAM_STATS_SAMTOOLS.out.stats      // channel: [ val(meta), path(stats) ]
-    flagstat = BAM_STATS_SAMTOOLS.out.flagstat   // channel: [ val(meta), path(flagstat) ]
-    idxstats = BAM_STATS_SAMTOOLS.out.idxstats   // channel: [ val(meta), path(idxstats) ]
-    coverage = BAM_STATS_SAMTOOLS.out.coverage   // channel: [ val(meta), path(coverage) ]
+    stats    = CRAM_STATS_SAMTOOLS.out.stats      // channel: [ val(meta), path(stats) ]
+    flagstat = CRAM_STATS_SAMTOOLS.out.flagstat   // channel: [ val(meta), path(flagstat) ]
+    idxstats = CRAM_STATS_SAMTOOLS.out.idxstats   // channel: [ val(meta), path(idxstats) ]
+    coverage = CRAM_STATS_SAMTOOLS.out.coverage   // channel: [ val(meta), path(coverage) ]
 
     versions = ch_versions                       // channel: [ versions.yml ]
 }
diff --git a/...f-core/bam_markduplicates_picard/meta.yml → ...local/cram_markduplicates_picard/meta.yml b/...f-core/bam_markduplicates_picard/meta.yml → ...local/cram_markduplicates_picard/meta.yml
@@ -1,5 +1,5 @@
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
-name: "bam_markduplicates_picard"
+name: "cram_markduplicates_picard"
 description: Picard MarkDuplicates, index BAM file and run samtools stats, flagstat and idxstats
 keywords:
   - markduplicates
@@ -12,7 +12,7 @@ components:
   - samtools/stats
   - samtools/idxstats
   - samtools/flagstat
-  - bam_stats_samtools
+  - cram_stats_samtools
 input:
   - ch_bam:
       description: |

diff --git a/..._markduplicates_picard/tests/main.nf.test → ..._markduplicates_picard/tests/main.nf.test b/..._markduplicates_picard/tests/main.nf.test → ..._markduplicates_picard/tests/main.nf.test
@@ -1,17 +1,17 @@
 nextflow_workflow {
 
-    name "Test Workflow BAM_MARKDUPLICATES_PICARD"
+    name "Test Workflow CRAM_MARKDUPLICATES_PICARD"
     script "../main.nf"
-    workflow "BAM_MARKDUPLICATES_PICARD"
+    workflow "CRAM_MARKDUPLICATES_PICARD"
 
     tag "picard"
     tag "picard/markduplicates"
     tag "subworkflows"
     tag "subworkflows_nfcore"
-    tag "bam_markduplicates_picard"
-    tag "subworkflows/bam_markduplicates_picard"
-    tag "subworkflows/bam_stats_samtools"
-    tag "bam_stats_samtools"
+    tag "cram_markduplicates_picard"
+    tag "subworkflows/cram_markduplicates_picard"
+    tag "subworkflows/cram_stats_samtools"
+    tag "cram_stats_samtools"
     tag "samtools"
     tag "samtools/flagstat"
     tag "samtools/idxstats"

diff --git a/...duplicates_picard/tests/main.nf.test.snap → ...duplicates_picard/tests/main.nf.test.snap b/...duplicates_picard/tests/main.nf.test.snap → ...duplicates_picard/tests/main.nf.test.snap
diff --git a/subworkflows/local/cram_markduplicates_picard/tests/tags.yml b/subworkflows/local/cram_markduplicates_picard/tests/tags.yml
@@ -0,0 +1,2 @@
+subworkflows/cram_markduplicates_picard:
+  - subworkflows/nf-core/cram_markduplicates_picard/**
diff --git a/subworkflows/local/cram_stats_samtools/bam_stats_samtools/main.nf b/subworkflows/local/cram_stats_samtools/bam_stats_samtools/main.nf
@@ -0,0 +1,37 @@
+CRAM_STATS_SAMTOOLS//
+// Run SAMtools stats, flagstat and idxstats
+//
+
+include { SAMTOOLS_STATS    } from '../../../modules/nf-core/samtools/stats/main'
+include { SAMTOOLS_IDXSTATS } from '../../../modules/nf-core/samtools/idxstats/main'
+include { SAMTOOLS_FLAGSTAT } from '../../../modules/nf-core/samtools/flagstat/main'
+include { SAMTOOLS_COVERAGE } from '../../../modules/nf-core/samtools/coverage/main'
+
+workflow CRAM_STATS_SAMTOOLS {
+    take:
+    ch_bam_crai // channel: [ val(meta), path(bam), path(crai) ]
+    ch_fasta    // channel: [ val(meta), path(fasta) ]
+
+    main:
+    ch_versions = Channel.empty()
+
+    SAMTOOLS_STATS ( ch_bam_crai, ch_fasta )
+    ch_versions = ch_versions.mix(SAMTOOLS_STATS.out.versions)
+
+    SAMTOOLS_FLAGSTAT ( ch_bam_crai )
+    ch_versions = ch_versions.mix(SAMTOOLS_FLAGSTAT.out.versions)
+
+    SAMTOOLS_IDXSTATS ( ch_bam_crai )
+    ch_versions = ch_versions.mix(SAMTOOLS_IDXSTATS.out.versions)
+
+    SAMTOOLS_COVERAGE ( ch_bam_crai )
+    ch_versions = ch_versions.mix(SAMTOOLS_COVERAGE.out.versions)
+
+    emit:
+    stats    = SAMTOOLS_STATS.out.stats       // channel: [ val(meta), path(stats) ]
+    flagstat = SAMTOOLS_FLAGSTAT.out.flagstat // channel: [ val(meta), path(flagstat) ]
+    idxstats = SAMTOOLS_IDXSTATS.out.idxstats // channel: [ val(meta), path(idxstats) ]
+    coverage = SAMTOOLS_COVERAGE.out.coverage // channel: [ val(meta), path(coverage) ]
+
+    versions = ch_versions                    // channel: [ path(versions.yml) ]
+}
diff --git a/...kflows/nf-core/bam_stats_samtools/main.nf → ...rkflows/local/cram_stats_samtools/main.nf b/...kflows/nf-core/bam_stats_samtools/main.nf → ...rkflows/local/cram_stats_samtools/main.nf
@@ -7,7 +7,7 @@ include { SAMTOOLS_IDXSTATS } from '../../../modules/nf-core/samtools/idxstats/m
 include { SAMTOOLS_FLAGSTAT } from '../../../modules/nf-core/samtools/flagstat/main'
 include { SAMTOOLS_COVERAGE } from '../../../modules/nf-core/samtools/coverage/main'
 
-workflow BAM_STATS_SAMTOOLS {
+workflow CRAM_STATS_SAMTOOLS {
     take:
     ch_bam_crai // channel: [ val(meta), path(bam), path(crai) ]
     ch_fasta    // channel: [ val(meta), path(fasta) ]

diff --git a/...flows/nf-core/bam_stats_samtools/meta.yml → ...kflows/local/cram_stats_samtools/meta.yml b/...flows/nf-core/bam_stats_samtools/meta.yml → ...kflows/local/cram_stats_samtools/meta.yml
@@ -1,5 +1,5 @@
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
-name: bam_stats_samtools
+name: cram_stats_samtools
 description: Produces comprehensive statistics from SAM/BAM/CRAM file
 keywords:
   - statistics

diff --git a/...ore/bam_stats_samtools/tests/main.nf.test → ...al/cram_stats_samtools/tests/main.nf.test b/...ore/bam_stats_samtools/tests/main.nf.test → ...al/cram_stats_samtools/tests/main.nf.test
@@ -1,18 +1,18 @@
 nextflow_workflow {
 
-    name "Test Workflow BAM_STATS_SAMTOOLS"
+    name "Test Workflow CRAM_STATS_SAMTOOLS"
     script "../main.nf"
-    workflow "BAM_STATS_SAMTOOLS"
+    workflow "CRAM_STATS_SAMTOOLS"
     tag "subworkflows"
     tag "subworkflows_nfcore"
-    tag "bam_stats_samtools"
-    tag "subworkflows/bam_stats_samtools"
+    tag "cram_stats_samtools"
+    tag "subworkflows/cram_stats_samtools"
     tag "samtools"
     tag "samtools/flagstat"
     tag "samtools/idxstats"
     tag "samtools/stats"
 
-    test("test_bam_stats_samtools_single_end") {
+    test("test_cram_stats_samtools_single_end") {
 
         when {
             params {
@@ -36,14 +36,14 @@ nextflow_workflow {
         then {
             assertAll(
                 { assert workflow.success},
-                { assert snapshot(workflow.out.stats).match("test_bam_stats_samtools_single_end_stats") },
-                { assert snapshot(workflow.out.flagstat).match("test_bam_stats_samtools_single_end_flagstats") },
-                { assert snapshot(workflow.out.idxstats).match("test_bam_stats_samtools_single_end_idxstats") }
+                { assert snapshot(workflow.out.stats).match("test_cram_stats_samtools_single_end_stats") },
+                { assert snapshot(workflow.out.flagstat).match("test_cram_stats_samtools_single_end_flagstats") },
+                { assert snapshot(workflow.out.idxstats).match("test_cram_stats_samtools_single_end_idxstats") }
             )
         }
     }
 
-    test("test_bam_stats_samtools_paired_end") {
+    test("test_cram_stats_samtools_paired_end") {
 
         when {
             params {
@@ -67,14 +67,14 @@ nextflow_workflow {
         then {
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(workflow.out.stats).match("test_bam_stats_samtools_paired_end_stats") },
-                { assert snapshot(workflow.out.flagstat).match("test_bam_stats_samtools_paired_end_flagstats") },
-                { assert snapshot(workflow.out.idxstats).match("test_bam_stats_samtools_paired_end_idxstats") }
+                { assert snapshot(workflow.out.stats).match("test_cram_stats_samtools_paired_end_stats") },
+                { assert snapshot(workflow.out.flagstat).match("test_cram_stats_samtools_paired_end_flagstats") },
+                { assert snapshot(workflow.out.idxstats).match("test_cram_stats_samtools_paired_end_idxstats") }
             )
         }
     }
 
-    test("test_bam_stats_samtools_paired_end_cram") {
+    test("test_cram_stats_samtools_paired_end_cram") {
 
         when {
             params {
@@ -98,9 +98,9 @@ nextflow_workflow {
         then {
             assertAll(
                 { assert workflow.success},
-                { assert snapshot(workflow.out.stats).match("test_bam_stats_samtools_paired_end_cram_stats") },
-                { assert snapshot(workflow.out.flagstat).match("test_bam_stats_samtools_paired_end_cram_flagstats") },
-                { assert snapshot(workflow.out.idxstats).match("test_bam_stats_samtools_paired_end_cram_idxstats") }
+                { assert snapshot(workflow.out.stats).match("test_cram_stats_samtools_paired_end_cram_stats") },
+                { assert snapshot(workflow.out.flagstat).match("test_cram_stats_samtools_paired_end_cram_flagstats") },
+                { assert snapshot(workflow.out.idxstats).match("test_cram_stats_samtools_paired_end_cram_idxstats") }
             )
         }
     }

diff --git a/...am_stats_samtools/tests/main.nf.test.snap → ...am_stats_samtools/tests/main.nf.test.snap b/...am_stats_samtools/tests/main.nf.test.snap → ...am_stats_samtools/tests/main.nf.test.snap
@@ -1,5 +1,5 @@
 {
-    "test_bam_stats_samtools_paired_end_cram_flagstats": {
+    "test_cram_stats_samtools_paired_end_cram_flagstats": {
         "content": [
             [
                 [
@@ -17,7 +17,7 @@
         },
         "timestamp": "2023-11-06T09:31:26.194017574"
     },
-    "test_bam_stats_samtools_paired_end_stats": {
+    "test_cram_stats_samtools_paired_end_stats": {
         "content": [
             [
                 [
@@ -35,7 +35,7 @@
         },
         "timestamp": "2024-02-13T16:45:06.230091746"
     },
-    "test_bam_stats_samtools_paired_end_flagstats": {
+    "test_cram_stats_samtools_paired_end_flagstats": {
         "content": [
             [
                 [
@@ -53,7 +53,7 @@
         },
         "timestamp": "2024-01-18T17:17:27.717482"
     },
-    "test_bam_stats_samtools_single_end_flagstats": {
+    "test_cram_stats_samtools_single_end_flagstats": {
         "content": [
             [
                 [
@@ -71,7 +71,7 @@
         },
         "timestamp": "2023-11-06T09:26:10.340046381"
     },
-    "test_bam_stats_samtools_paired_end_cram_idxstats": {
+    "test_cram_stats_samtools_paired_end_cram_idxstats": {
         "content": [
             [
                 [
@@ -89,7 +89,7 @@
         },
         "timestamp": "2023-11-06T09:31:26.207052003"
     },
-    "test_bam_stats_samtools_single_end_stats": {
+    "test_cram_stats_samtools_single_end_stats": {
         "content": [
             [
                 [
@@ -107,7 +107,7 @@
         },
         "timestamp": "2024-02-13T16:44:57.442208382"
     },
-    "test_bam_stats_samtools_paired_end_idxstats": {
+    "test_cram_stats_samtools_paired_end_idxstats": {
         "content": [
             [
                 [
@@ -125,7 +125,7 @@
         },
         "timestamp": "2024-01-18T17:17:27.726719"
     },
-    "test_bam_stats_samtools_single_end_idxstats": {
+    "test_cram_stats_samtools_single_end_idxstats": {
         "content": [
             [
                 [
@@ -143,7 +143,7 @@
         },
         "timestamp": "2023-11-06T09:26:10.349439801"
     },
-    "test_bam_stats_samtools_paired_end_cram_stats": {
+    "test_cram_stats_samtools_paired_end_cram_stats": {
         "content": [
             [
                 [
@@ -161,4 +161,4 @@
         },
         "timestamp": "2024-02-13T16:45:14.997164209"
     }
-}
+}
diff --git a/subworkflows/local/cram_stats_samtools/tests/tags.yml b/subworkflows/local/cram_stats_samtools/tests/tags.yml
@@ -0,0 +1,2 @@
+subworkflows/cram_stats_samtools:
+  - subworkflows/nf-core/cram_stats_samtools/**
diff --git a/subworkflows/nf-core/bam_markduplicates_picard/tests/tags.yml b/subworkflows/nf-core/bam_markduplicates_picard/tests/tags.yml
diff --git a/subworkflows/nf-core/bam_stats_samtools/tests/tags.yml b/subworkflows/nf-core/bam_stats_samtools/tests/tags.yml
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		subworkflows/cram_markduplicates_picard:
		- subworkflows/nf-core/cram_markduplicates_picard/**
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		subworkflows/cram_stats_samtools:
		- subworkflows/nf-core/cram_stats_samtools/**