Update mirtop modules and subworkflow (#6635)

* add arity to mirtop/gff * add prefix to mirtop output * update tests and snapshots * update yml
nf-core · Sep 13, 2024 · 43b2b70 · 43b2b70
1 parent aa8c39b
commit 43b2b70
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Showing 12 changed files with 35 additions and 76 deletions.
diff --git a/modules/nf-core/mirtop/counts/tests/main.nf.test b/modules/nf-core/mirtop/counts/tests/main.nf.test
@@ -38,7 +38,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = MIRTOP_GFF.out.mirtop_gff
+                input[0] = MIRTOP_GFF.out.gff
                 input[1] = [
                     [ id:'hairpin'], // meta map
                     file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/mirtop/hairpin_mirtop.fa", checkIfExists: true),
@@ -72,7 +72,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = MIRTOP_GFF.out.mirtop_gff
+                input[0] = MIRTOP_GFF.out.gff
                 input[1] = [
                     [ id:'hairpin'], // meta map
                     file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/mirtop/hairpin_mirtop.fa", checkIfExists: true),

diff --git a/modules/nf-core/mirtop/export/tests/main.nf.test b/modules/nf-core/mirtop/export/tests/main.nf.test
@@ -37,7 +37,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = MIRTOP_GFF.out.mirtop_gff
+                input[0] = MIRTOP_GFF.out.gff
                 input[1] = [
                     [ id:'hairpin'], // meta map
                     file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/mirtop/hairpin_mirtop.fa", checkIfExists: true),
@@ -66,7 +66,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = MIRTOP_GFF.out.mirtop_gff
+                input[0] = MIRTOP_GFF.out.gff
                 input[1] = [
                     [ id:'hairpin'], // meta map
                     file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/mirtop/hairpin_mirtop.fa", checkIfExists: true),

diff --git a/modules/nf-core/mirtop/export/tests/main.nf.test.snap b/modules/nf-core/mirtop/export/tests/main.nf.test.snap
@@ -62,7 +62,7 @@
                         {
                             "id": "sample_sim_isomir_bam"
                         },
-                        "mirtop_rawData.tsv:md5,efbcbe67716a4a56f89e538af2251dcc"
+                        "sample_sim_isomir_bam_mirtop_rawData.tsv:md5,efbcbe67716a4a56f89e538af2251dcc"
                     ]
                 ],
                 "1": [
@@ -82,7 +82,7 @@
                         {
                             "id": "sample_sim_isomir_bam"
                         },
-                        "mirtop_rawData.tsv:md5,efbcbe67716a4a56f89e538af2251dcc"
+                        "sample_sim_isomir_bam_mirtop_rawData.tsv:md5,efbcbe67716a4a56f89e538af2251dcc"
                     ]
                 ],
                 "vcf": [
@@ -97,6 +97,6 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-09-03T15:25:24.528528611"
+        "timestamp": "2024-09-12T23:12:49.612315132"
     }
 }
diff --git a/modules/nf-core/mirtop/gff/main.nf b/modules/nf-core/mirtop/gff/main.nf
@@ -8,13 +8,12 @@ process MIRTOP_GFF {
         'biocontainers/mulled-v2-0c13ef770dd7cc5c76c2ce23ba6669234cf03385:63be019f50581cc5dfe4fc0f73ae50f2d4d661f7-0' }"
 
     input:
-    tuple val(meta), path(bam)
+    tuple val(meta), path(bam, arity:'1..*')
     tuple val(meta2), path(hairpin)
     tuple val(meta3), path(gtf), val(species)
 
     output:
-    tuple val(meta), path("mirtop/${bam.baseName}.gff")  , emit: sample_gff
-    tuple val(meta), path("mirtop/mirtop.gff")           , emit: mirtop_gff
+    tuple val(meta), path("mirtop/*mirtop.gff")           , emit: gff
     path "versions.yml"                                  , emit: versions
 
     when:
@@ -33,6 +32,8 @@ process MIRTOP_GFF {
         -o mirtop \\
         $bam
 
+    mv mirtop/mirtop.gff mirtop/${prefix}_mirtop.gff
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         mirtop: \$(echo \$(mirtop --version 2>&1) | sed 's/^.*mirtop //')
@@ -45,7 +46,6 @@ process MIRTOP_GFF {
     """
     mkdir mirtop
     touch mirtop/mirtop.gff
-    touch mirtop/sim_isomir_sort.gff
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/nf-core/mirtop/gff/meta.yml b/modules/nf-core/mirtop/gff/meta.yml
@@ -46,11 +46,7 @@ output:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
-  - mirtop_gff:
-      type: file
-      description: GFF file
-      pattern: "*.{gff}"
-  - sample_gff:
+  - gff:
       type: file
       description: GFF file
       pattern: "*.{gff}"

diff --git a/modules/nf-core/mirtop/gff/tests/main.nf.test b/modules/nf-core/mirtop/gff/tests/main.nf.test
@@ -35,12 +35,11 @@ nextflow_process {
                 { assert process.success },
                 { assert snapshot(
                     process.out.bam,
-                    file(process.out.sample_gff[0][1]).readLines().findAll { it.contains("hsa-let-7a-2	miRBasev21	isomiR	3	25	0	+	.	Read TTGAGGTAGTAGGTTGTATAGTT; UID iso-23-Z0S31NSL0E; Name hsa-let-7a-5p;Parent hsa-let-7a-2; Variant iso_5p:-1; Cigar 23M;Expression 0; Filter Pass; Hits 1;") },
                     process.out.versions,
                         ).match()
                         },
                 // md5sum is not stable, order of elements in section "variant" may change
-                { assert file(process.out.mirtop_gff[0][1]).readLines().findAll { it.contains("iso-24-5URPV39QFB") }}
+                { assert file(process.out.gff[0][1]).readLines().findAll { it.contains("iso-24-5URPV39QFB") }}
                 )
         }
 

diff --git a/modules/nf-core/mirtop/gff/tests/main.nf.test.snap b/modules/nf-core/mirtop/gff/tests/main.nf.test.snap
@@ -3,40 +3,24 @@
         "content": [
             {
                 "0": [
-                    [
-                        {
-                            "id": "sample_sim_isomir_bam"
-                        },
-                        "sim_isomir_sort.gff:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "1": [
                     [
                         {
                             "id": "sample_sim_isomir_bam"
                         },
                         "mirtop.gff:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "2": [
+                "1": [
                     "versions.yml:md5,d16ade25d46f8d12e200e124205afefc"
                 ],
-                "mirtop_gff": [
+                "gff": [
                     [
                         {
                             "id": "sample_sim_isomir_bam"
                         },
                         "mirtop.gff:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "sample_gff": [
-                    [
-                        {
-                            "id": "sample_sim_isomir_bam"
-                        },
-                        "sim_isomir_sort.gff:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
                 "versions": [
                     "versions.yml:md5,d16ade25d46f8d12e200e124205afefc"
                 ]
@@ -46,14 +30,11 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-09-03T12:47:11.610449763"
+        "timestamp": "2024-09-12T22:40:30.542921953"
     },
     "isomir - bam": {
         "content": [
             null,
-            [
-                "hsa-let-7a-2\tmiRBasev21\tisomiR\t3\t25\t0\t+\t.\tRead TTGAGGTAGTAGGTTGTATAGTT; UID iso-23-Z0S31NSL0E; Name hsa-let-7a-5p;Parent hsa-let-7a-2; Variant iso_5p:-1; Cigar 23M;Expression 0; Filter Pass; Hits 1;"
-            ],
             [
                 "versions.yml:md5,d16ade25d46f8d12e200e124205afefc"
             ]
@@ -62,6 +43,6 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-09-06T21:42:47.26306174"
+        "timestamp": "2024-09-12T22:38:09.903017316"
     }
 }
diff --git a/modules/nf-core/mirtop/stats/meta.yml b/modules/nf-core/mirtop/stats/meta.yml
@@ -39,6 +39,10 @@ output:
       type: file
       description: TXT file with stats
       pattern: "*.{txt}"
+  - log:
+      type: file
+      description: log file with stats
+      pattern: "*.{log}"
 
 authors:
   - "@atrigila"

diff --git a/modules/nf-core/mirtop/stats/tests/main.nf.test b/modules/nf-core/mirtop/stats/tests/main.nf.test
@@ -8,31 +8,8 @@ nextflow_process {
     tag "modules"
     tag "modules_nfcore"
     tag "mirtop"
-    tag "mirtop/gff"
     tag "mirtop/stats"
 
-    setup {
-            run("MIRTOP_GFF") {
-                script "../../gff/main.nf"
-                process {
-                """
-                input[0] = [
-                    [ id:'sample_sim_isomir_bam'], // meta map
-                    file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/mirtop/sim_isomir_sort.bam", checkIfExists: true),
-                ]
-                input[1] = [
-                    [ id:'hairpin'], // meta map
-                    file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/mirtop/hairpin_mirtop.fa", checkIfExists: true),
-                ]
-                input[2] = [
-                    [ id:'hsa' ], // meta map
-                    file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/mirtop/hsa.gff3", checkIfExists: true),
-                "hsa"]
-                """
-            }
-            }
-        }
-
     test("isomir - bam") {
 
         when {

diff --git a/subworkflows/nf-core/bam_stats_mirna_mirtop/main.nf b/subworkflows/nf-core/bam_stats_mirna_mirtop/main.nf
@@ -16,19 +16,20 @@ workflow BAM_STATS_MIRNA_MIRTOP {
     ch_versions = Channel.empty()
 
     MIRTOP_GFF ( ch_bam, ch_hairpin, ch_gtf_species )
-    ch_versions = ch_versions.mix(MIRTOP_GFF.out.versions.first())
+    ch_versions = ch_versions.mix(MIRTOP_GFF.out.versions)
 
-    MIRTOP_COUNTS ( MIRTOP_GFF.out.mirtop_gff, ch_hairpin, ch_gtf_species )
-    ch_versions = ch_versions.mix(MIRTOP_COUNTS.out.versions.first())
+    MIRTOP_COUNTS ( MIRTOP_GFF.out.gff, ch_hairpin, ch_gtf_species )
+    ch_versions = ch_versions.mix(MIRTOP_COUNTS.out.versions)
 
-    MIRTOP_EXPORT ( MIRTOP_GFF.out.mirtop_gff, ch_hairpin, ch_gtf_species )
-    ch_versions = ch_versions.mix(MIRTOP_EXPORT.out.versions.first())
+    MIRTOP_EXPORT ( MIRTOP_GFF.out.gff, ch_hairpin, ch_gtf_species )
+    ch_versions = ch_versions.mix(MIRTOP_EXPORT.out.versions)
 
-    MIRTOP_STATS ( MIRTOP_GFF.out.mirtop_gff )
-    ch_versions = ch_versions.mix(MIRTOP_STATS.out.versions.first())
+    MIRTOP_STATS ( MIRTOP_GFF.out.gff )
+    ch_versions = ch_versions.mix(MIRTOP_STATS.out.versions)
 
     emit:
-    rawdata_tsv    = MIRTOP_EXPORT.out.tsv                  // channel: [ val(meta), [ tsv ] ]
+    isomirs        = MIRTOP_EXPORT.out.tsv                  // channel: [ val(meta), [ tsv ] ]
+    counts         = MIRTOP_COUNTS.out.tsv                  // channel: [ val(meta), [ tsv ] ]
     stats_txt      = MIRTOP_STATS.out.txt                   // channel: [ val(meta), [ txt ] ]
     stats_log      = MIRTOP_STATS.out.log                   // channel: [ val(meta), [ log ] ]
     versions       = ch_versions                            // channel: [ versions.yml ]

diff --git a/subworkflows/nf-core/bam_stats_mirna_mirtop/tests/main.nf.test b/subworkflows/nf-core/bam_stats_mirna_mirtop/tests/main.nf.test
@@ -39,10 +39,11 @@ nextflow_workflow {
             assertAll(
                 { assert workflow.success},
                 { assert snapshot(
-                    workflow.out.rawdata_tsv,
+                    workflow.out.isomirs,
                     workflow.out.stats_txt,
                     workflow.out.stats_log,
-                    workflow.out.versions).match() }
+                    workflow.out.versions).match() },
+                { assert path("${workflow.out.counts[0][1]}").exists() }
             )
         }
     }

diff --git a/subworkflows/nf-core/bam_stats_mirna_mirtop/tests/main.nf.test.snap b/subworkflows/nf-core/bam_stats_mirna_mirtop/tests/main.nf.test.snap
@@ -6,7 +6,7 @@
                     {
                         "id": "sample_sim_isomir_bam"
                     },
-                    "mirtop_rawData.tsv:md5,4a065e444c54b0e816352bf1640594dd"
+                    "sample_sim_isomir_bam_mirtop_rawData.tsv:md5,4a065e444c54b0e816352bf1640594dd"
                 ]
             ],
             [
@@ -36,6 +36,6 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-09-04T21:31:21.204039357"
+        "timestamp": "2024-09-12T23:13:48.308574263"
     }
 }