remove implicit params use in sub-wf

subworkflows/nf-core/fasta_index_bismark_bwameth/main.nf

@@ -7,10 +7,12 @@ include { SAMTOOLS_FAIDX            } from '../../../modules/nf-core/samtools/fa
 workflow FASTA_INDEX_BISMARK_BWAMETH {
 
     take:
-    fasta         // channel: [ val(meta), [ fasta ] ]
-    fasta_index   // channel: [ val(meta), [ fasta index ] ]
-    bismark_index // channel: [ val(meta), [ bismark index ] ]
-    bwameth_index // channel: [ val(meta), [ bwameth index ] ]
+    fasta            // channel: [ val(meta), [ fasta ] ]
+    fasta_index      // channel: [ val(meta), [ fasta index ] ]
+    bismark_index    // channel: [ val(meta), [ bismark index ] ]
+    bwameth_index    // channel: [ val(meta), [ bwameth index ] ]
+    aligner          // string: bismark, bismark_hisat or bwameth
+    collecthsmetrics // boolean: whether to run picard collecthsmetrics
 
     main:
 
@@ -20,31 +22,41 @@ workflow FASTA_INDEX_BISMARK_BWAMETH {
     ch_bwameth_index = Channel.empty()
     ch_versions      = Channel.empty()
 
-    if (fasta.toString().endsWith('.gz')) {
-        GUNZIP (
-            [ [:], file(fasta, checkIfExists: true) ]
-        )
-        ch_fasta    = GUNZIP.out.gunzip
-        ch_versions = ch_versions.mix(GUNZIP.out.versions)
-    } else {
-        ch_fasta    = Channel.value([[:], file(fasta, checkIfExists: true)])
-    }
+    // Check if fasta file is gzipped and decompress if needed
+    fasta
+        .branch {
+            gzipped: it[1].toString().endsWith('.gz')
+            unzipped: true
+        }
+        .set { ch_fasta_branched }
+
+    GUNZIP (
+        ch_fasta_branched.gzipped.ifEmpty([])
+    )
+
+    ch_fasta    = ch_fasta_branched.unzipped.mix(GUNZIP.out.gunzip)
+    ch_versions = ch_versions.mix(GUNZIP.out.versions)
 
     // Aligner: bismark or bismark_hisat
-    if( params.aligner =~ /bismark/ ){
+    if( aligner =~ /bismark/ ){
         /*
          * Generate bismark index if not supplied
          */
         if (bismark_index) {
-            if (bismark_index.toString().endsWith('.gz')) {
-                UNTAR (
-                    [ [:], file(bismark_index, checkIfExists: true) ]
-                )
-                ch_bismark_index = UNTAR.out.untar
-                ch_versions      = ch_versions.mix(UNTAR.out.versions)
-            } else {
-                ch_bismark_index = Channel.value([[:], file(bismark_index, checkIfExists: true)])
-            }
+            // Handle channel-based bismark index
+            bismark_index
+                .branch {
+                    gzipped: it[1].toString().endsWith('.gz')
+                    unzipped: true
+                }
+                .set { ch_bismark_index_branched }
+
+            UNTAR (
+                ch_bismark_index_branched.gzipped.ifEmpty([])
+            )
+
+            ch_bismark_index = ch_bismark_index_branched.unzipped.mix(UNTAR.out.untar)
+            ch_versions      = ch_versions.mix(UNTAR.out.versions)
         } else {
             BISMARK_GENOMEPREPARATION (
                 ch_fasta
@@ -55,20 +67,25 @@ workflow FASTA_INDEX_BISMARK_BWAMETH {
     }
 
     // Aligner: bwameth
-    else if ( params.aligner == 'bwameth' ){
+    else if ( aligner == 'bwameth' ){
         /*
          * Generate bwameth index if not supplied
          */
         if (bwameth_index) {
-            if (bwameth_index.toString().endsWith('.gz')) {
-                UNTAR (
-                    [ [:], file(bwameth_index, checkIfExists: true) ]
-                )
-                ch_bwameth_index = UNTAR.out.untar
-                ch_versions      = ch_versions.mix(UNTAR.out.versions)
-            } else {
-                ch_bwameth_index = Channel.value([[:], file(bwameth_index, checkIfExists: true)])
-            }
+            // Handle channel-based bwameth index
+            bwameth_index
+                .branch {
+                    gzipped: it[1].toString().endsWith('.gz')
+                    unzipped: true
+                }
+                .set { ch_bwameth_index_branched }
+
+            UNTAR (
+                ch_bwameth_index_branched.gzipped.ifEmpty([])
+            )
+
+            ch_bwameth_index = ch_bwameth_index_branched.unzipped.mix(UNTAR.out.untar)
+            ch_versions      = ch_versions.mix(UNTAR.out.versions)
         } else {
             BWAMETH_INDEX (
                 ch_fasta
@@ -81,15 +98,15 @@ workflow FASTA_INDEX_BISMARK_BWAMETH {
     /*
     * Generate fasta index if not supplied for bwameth workflow or picard collecthsmetrics tool
     */
-    if (params.aligner == 'bwameth' | params.run_picard_collecthsmetrics) {
+    if (aligner == 'bwameth' | collecthsmetrics) {
         // already exising fasta index
         if (fasta_index) {
-            ch_fasta_index = Channel.value(file(fasta_index, checkIfExists: true))
+            ch_fasta_index = fasta_index
         } else {
             SAMTOOLS_FAIDX(
                 ch_fasta,
                 [[:], []],
-                false // No sizes generation
+                false
             )
             ch_fasta_index = SAMTOOLS_FAIDX.out.fai
             ch_versions    = ch_versions.mix(SAMTOOLS_FAIDX.out.versions)

subworkflows/nf-core/fasta_index_bismark_bwameth/meta.yml

@@ -35,6 +35,14 @@ input:
       description: |
         Bwameth genome index files
         Structure: [ val(meta), path(bwameth_index) ]
+  - aligner:
+      type: string
+      description: |
+        Aligner name (bismark, bismark_hisat, or bwameth)
+  - collecthsmetrics:
+      type: boolean
+      description: |
+        Whether to run picard collecthsmetrics tool
 output:
   - fasta:
       type: file
@@ -68,5 +76,7 @@ output:
       pattern: "versions.yml"
 authors:
   - "@sateeshperi"
+  - "dcarrillox"
 maintainers:
   - "@sateeshperi"
+  - "@dcarrillox"

subworkflows/nf-core/fasta_index_bismark_bwameth/tests/main.nf.test

@@ -17,15 +17,14 @@ nextflow_workflow {
     test("Params: bismark | download bismark index (bowtie2)") {
 
         when {
-            params {
-                aligner = "bismark"
-            }
             workflow {
                 """
-                input[0] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.gz', checkIfExists: true)
+                input[0] = Channel.fromPath('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.gz', checkIfExists: true).map { it -> [ [:], it ] }
                 input[1] = [] // fasta_index
-                input[2] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/Bowtie2_Index.tar.gz', checkIfExists: true)
+                input[2] = Channel.fromPath('https://github.com/nf-core/test-datasets/raw/methylseq/reference/Bowtie2_Index.tar.gz', checkIfExists: true).map { it -> [ [:], it ] }
                 input[3] = [] // bwameth_index
+                input[4] = "bismark" // aligner
+                input[5] = false // collecthsmetrics
                 """
             }
         }
@@ -47,15 +46,14 @@ nextflow_workflow {
     test("Params: bismark | generate bismark index (bowtie2)") {
 
         when {
-            params {
-                aligner = "bismark"
-            }
             workflow {
                 """
-                input[0] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.gz', checkIfExists: true)
+                input[0] = Channel.fromPath('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.gz', checkIfExists: true).map { it -> [ [:], it ] }
                 input[1] = [] // fasta_index
                 input[2] = [] // bismark_index
                 input[3] = [] // bwameth_index
+                input[4] = "bismark" // aligner
+                input[5] = false // collecthsmetrics
                 """
             }
         }
@@ -77,15 +75,14 @@ nextflow_workflow {
     test("Params: bismark_hisat | download bismark index (hisat2)") {
 
         when {
-            params {
-                aligner = "bismark_hisat"
-            }
             workflow {
                 """
-                input[0] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.gz', checkIfExists: true)
+                input[0] = Channel.fromPath('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.gz', checkIfExists: true).map { it -> [ [:], it ] }
                 input[1] = [] // fasta_index
-                input[2] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/Hisat2_Index.tar.gz', checkIfExists: true)
+                input[2] = Channel.fromPath('https://github.com/nf-core/test-datasets/raw/methylseq/reference/Hisat2_Index.tar.gz', checkIfExists: true).map { it -> [ [:], it ] }
                 input[3] = [] // bwameth_index
+                input[4] = "bismark_hisat" // aligner
+                input[5] = false // collecthsmetrics
                 """
             }
         }
@@ -107,46 +104,14 @@ nextflow_workflow {
     test("Params: bismark_hisat | generate bismark index (hisat2)") {
 
         when {
-            params {
-                aligner = "bismark_hisat"
-            }
             workflow {
                 """
-                input[0] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.gz', checkIfExists: true)
+                input[0] = Channel.fromPath('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.gz', checkIfExists: true).map { it -> [ [:], it ] }
                 input[1] = [] // fasta_index
-                input[2] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/Hisat2_Index.tar.gz', checkIfExists: true)
-                input[3] = [] // bwameth_index
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success},
-                { assert snapshot(
-                    workflow.out.fasta,
-                    workflow.out.fasta_index,
-                    workflow.out.bismark_index,
-                    workflow.out.bwameth_index,
-                    workflow.out.versions
-                    ).match() }
-            )
-        }
-    }
-
-    test("Params: bismark | download bismark index (bowtie2) | run_picard_collecthsmetrics") {
-
-        when {
-            params {
-                aligner = "bismark"
-                run_picard_collecthsmetrics = true
-            }
-            workflow {
-                """
-                input[0] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.gz', checkIfExists: true)
-                input[1] = [] // fasta_index
-                input[2] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/Bowtie2_Index.tar.gz', checkIfExists: true)
+                input[2] = Channel.fromPath('https://github.com/nf-core/test-datasets/raw/methylseq/reference/Hisat2_Index.tar.gz', checkIfExists: true).map { it -> [ [:], it ] }
                 input[3] = [] // bwameth_index
+                input[4] = "bismark_hisat" // aligner
+                input[5] = false // collecthsmetrics
                 """
             }
         }
@@ -168,15 +133,14 @@ nextflow_workflow {
     test("Params: bwameth | download fasta index | download bwameth index") {
 
         when {
-            params {
-                aligner = "bwameth"
-            }
             workflow {
                 """
-                input[0] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.gz', checkIfExists: true)
-                input[1] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.fai', checkIfExists: true)
+                input[0] = Channel.fromPath('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.gz', checkIfExists: true).map { it -> [ [:], it ] }
+                input[1] = Channel.fromPath('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.fai', checkIfExists: true).map { it -> [ [:], it ] }
                 input[2] = [] // bismark index
-                input[3] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/Bwameth_Index.tar.gz', checkIfExists: true)
+                input[3] = Channel.fromPath('https://github.com/nf-core/test-datasets/raw/methylseq/reference/Bwameth_Index.tar.gz', checkIfExists: true).map { it -> [ [:], it ] }
+                input[4] = "bwameth" // aligner
+                input[5] = false // collecthsmetrics
                 """
             }
         }
@@ -198,15 +162,14 @@ nextflow_workflow {
     test("Params: bwameth | generate fasta index | download bwameth index") {
 
         when {
-            params {
-                aligner = "bwameth"
-            }
             workflow {
                 """
-                input[0] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.gz', checkIfExists: true)
+                input[0] = Channel.fromPath('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.gz', checkIfExists: true).map { it -> [ [:], it ] }
                 input[1] = [] //fasta index
                 input[2] = [] // bismark index
-                input[3] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/Bwameth_Index.tar.gz', checkIfExists: true)
+                input[3] = Channel.fromPath('https://github.com/nf-core/test-datasets/raw/methylseq/reference/Bwameth_Index.tar.gz', checkIfExists: true).map { it -> [ [:], it ] }
+                input[4] = "bwameth" // aligner
+                input[5] = false // collecthsmetrics
                 """
             }
         }
@@ -228,15 +191,14 @@ nextflow_workflow {
     test("Params: bwameth | generate fasta index | generate bwameth index") {
 
         when {
-            params {
-                aligner = "bwameth"
-            }
             workflow {
                 """
-                input[0] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.gz', checkIfExists: true)
+                input[0] = Channel.fromPath('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.gz', checkIfExists: true).map { it -> [ [:], it ] }
                 input[1] = [] // fasta_index
                 input[2] = [] // bismark index
                 input[3] = [] // bwameth index
+                input[4] = "bwameth" // aligner
+                input[5] = false // collecthsmetrics
                 """
             }
         }
@@ -255,19 +217,17 @@ nextflow_workflow {
         }
     }
 
-    test("Params: bwameth | generate fasta index | download bwameth index | run_picard_collecthsmetrics") {
+    test("Params: bwameth | generate fasta index | download bwameth index | collecthsmetrics") {
 
         when {
-            params {
-                aligner = "bwameth"
-                run_picard_collecthsmetrics = true
-            }
             workflow {
                 """
-                input[0] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.gz', checkIfExists: true)
+                input[0] = Channel.fromPath('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.gz', checkIfExists: true).map { it -> [ [:], it ] }
                 input[1] = [] //fasta index
                 input[2] = [] // bismark index
-                input[3] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/Bwameth_Index.tar.gz', checkIfExists: true)
+                input[3] = Channel.fromPath('https://github.com/nf-core/test-datasets/raw/methylseq/reference/Bwameth_Index.tar.gz', checkIfExists: true).map { it -> [ [:], it ] }
+                input[4] = "bwameth" // aligner
+                input[5] = true // collecthsmetrics
                 """
             }
         }