🔀 Merge pull request #31 from cnr-ibba/issue-30

pass *meta* information for genome input in freebayes modules
cnr-ibba · Dec 20, 2023 · 10aac07 · 10aac07
2 parents 9c8b0ee + 7dd9ff0
commit 10aac07
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Showing 16 changed files with 83 additions and 27 deletions.
diff --git a/modules/cnr-ibba/freebayes/chunk/main.nf b/modules/cnr-ibba/freebayes/chunk/main.nf
@@ -10,12 +10,12 @@ process FREEBAYES_CHUNK {
         'biocontainers/freebayes:1.3.6--hb089aa1_0' }"
 
     input:
-    tuple val(meta), val(region)
-    tuple val(sample_meta), path(bam)
-    tuple val(sample_meta), path(bai)
-    tuple val(sample_meta), path(bam_list)
-    path(genome_fasta)
-    path(genome_fasta_fai)
+    tuple val(meta),  val(region)
+    tuple val(meta2), path(bam)
+    tuple val(meta2), path(bai)
+    tuple val(meta2), path(bam_list)
+    tuple val(meta3), path(genome_fasta)
+    tuple val(meta3), path(genome_fasta_fai)
 
     output:
     tuple val(meta), path("*.vcf.gz")     , emit: vcf

diff --git a/modules/cnr-ibba/freebayes/chunk/meta.yml b/modules/cnr-ibba/freebayes/chunk/meta.yml
@@ -22,7 +22,7 @@ input:
       description: |
         Groovy Map containing information on a region
         e.g. [ id:'test', single_end:false ]
-  - sample_meta:
+  - meta2:
       type: map
       description: |
         Groovy Map containing sample information
@@ -42,6 +42,11 @@ input:
       type: file
       description: A txt file in which all bam file names are described
       pattern: "*.list.txt"
+  - meta3:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. [ id:'genome' ]
   - genome_fasta:
       type: file
       description: The genome fasta file (not compressed)
@@ -55,7 +60,7 @@ output:
   - meta:
       type: map
       description: |
-        Groovy Map containing sample information
+        Groovy Map containing information on a region
         e.g. [ id:'test', single_end:false ]
   - vcf:
       type: file

diff --git a/modules/cnr-ibba/freebayes/multi/main.nf b/modules/cnr-ibba/freebayes/multi/main.nf
@@ -9,8 +9,8 @@ process FREEBAYES_MULTI {
     input:
     tuple val(meta), path(bam)
     tuple val(meta), path(bai)
-    path(genome_fasta)
-    path(genome_fasta_fai)
+    tuple val(meta2), path(genome_fasta)
+    tuple val(meta2), path(genome_fasta_fai)
 
     output:
     tuple val(meta), path("*.vcf.gz")    , emit: vcf

diff --git a/modules/cnr-ibba/freebayes/multi/meta.yml b/modules/cnr-ibba/freebayes/multi/meta.yml
@@ -30,6 +30,11 @@ input:
       type: file
       description: A list of BAM index files
       pattern: "*.{bai}"
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. [ id:'genome' ]
   - genome_fasta:
       type: file
       description: The genome fasta file (not compressed)

diff --git a/modules/cnr-ibba/freebayes/single/main.nf b/modules/cnr-ibba/freebayes/single/main.nf
@@ -11,8 +11,8 @@ process FREEBAYES_SINGLE {
     input:
     tuple val(meta), path(bam), path(bai)
     tuple val(meta), path(coverage)
-    path(genome_fasta)
-    path(genome_fasta_fai)
+    tuple val(meta2), path(genome_fasta)
+    tuple val(meta2), path(genome_fasta_fai)
     val(num_regions)
 
     output:

diff --git a/modules/cnr-ibba/freebayes/single/meta.yml b/modules/cnr-ibba/freebayes/single/meta.yml
@@ -34,6 +34,11 @@ input:
       type: file
       description: Bamtools coverage output
       pattern: "*.{txt}"
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. [ id:'genome' ]
   - genome_fasta:
       type: file
       description: The genome fasta file (not compressed)

diff --git a/modules/cnr-ibba/freebayes/splitbam/main.nf b/modules/cnr-ibba/freebayes/splitbam/main.nf
@@ -9,8 +9,8 @@ process FREEBAYES_SPLITBAM {
     input:
     tuple val(meta), path(bam)
     tuple val(meta), path(bai)
-    path(genome_fasta)
-    path(genome_fasta_fai)
+    tuple val(meta2), path(genome_fasta)
+    tuple val(meta2), path(genome_fasta_fai)
 
     output:
     tuple val(meta), path("*.list.txt"), emit: bam_list

diff --git a/modules/cnr-ibba/freebayes/splitbam/meta.yml b/modules/cnr-ibba/freebayes/splitbam/meta.yml
@@ -27,6 +27,11 @@ input:
       type: file
       description: A list of BAM index files
       pattern: "*.{bai}"
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. [ id:'genome' ]
   - genome_fasta:
       type: file
       description: The genome fasta file (not compressed)

diff --git a/subworkflows/cnr-ibba/freebayes_parallel/main.nf b/subworkflows/cnr-ibba/freebayes_parallel/main.nf
@@ -11,8 +11,8 @@ workflow FREEBAYES_PARALLEL {
     take:
     bam     // channel: [ val(meta), [ bam/cram ]]
     bai     // channel: [ val(meta), [ bai/crai ]]
-    fasta   // channel: [ fasta ]
-    fai     // channel: [ fai ]
+    fasta   // channel: [ val(meta2), fasta ]
+    fai     // channel: [ val(meta2), fai ]
 
     main:
     ch_versions = Channel.empty()

diff --git a/subworkflows/cnr-ibba/freebayes_parallel/meta.yml b/subworkflows/cnr-ibba/freebayes_parallel/meta.yml
@@ -19,6 +19,11 @@ input:
       type: path
       description: A list of BAM index files
       pattern: "*.{bai}"
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. [ id:'genome' ]
   - genome_fasta:
       type: path
       description: The genome fasta file (not compressed)

diff --git a/tests/modules/cnr-ibba/freebayes/chunk/main.nf b/tests/modules/cnr-ibba/freebayes/chunk/main.nf
@@ -20,9 +20,15 @@ workflow test_freebayes_chunk {
     bam_ch = Channel.of(bam).map{ it -> [[id: "all.fb"], it]}
     bai_ch = Channel.of(bai).map{ it -> [[id: "all.fb"], it]}
 
-    genome_fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    genome_fasta = [
+        [ id:'genome' ],
+        file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    ]
 
-    genome_fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    genome_fasta_fai = [
+        [ id:'genome' ],
+        file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    ]
 
     FREEBAYES_SPLITBAM ( bam_ch, bai_ch, genome_fasta, genome_fasta_fai )
 

diff --git a/tests/modules/cnr-ibba/freebayes/chunk/test.yml b/tests/modules/cnr-ibba/freebayes/chunk/test.yml
@@ -9,6 +9,6 @@
     - path: output/freebayes/all.fb.regions.txt
       md5sum: e4cd6cbdb91d5205fcefcc7bc068d3e5
     - path: output/freebayes/chr22:0-40001.vcf.gz
-      md5sum: fba544980eebf86c66460c40f48d7809
+      md5sum: 8727d6512d790382b39e9ff13ac26ef0
     - path: output/freebayes/chr22:0-40001.vcf.gz.tbi
       md5sum: 83b1d5e5b36d61529d9d2d69cd4babc5
diff --git a/tests/modules/cnr-ibba/freebayes/multi/main.nf b/tests/modules/cnr-ibba/freebayes/multi/main.nf
@@ -20,9 +20,15 @@ workflow test_freebayes_multi {
     bam_ch = Channel.of(bam).map{ it -> [[id: "all.fb"], it]}
     bai_ch = Channel.of(bai).map{ it -> [[id: "all.fb"], it]}
 
-    genome_fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    genome_fasta = [
+        [ id:'genome' ],
+        file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    ]
 
-    genome_fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    genome_fasta_fai = [
+        [ id:'genome' ],
+        file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    ]
 
     FREEBAYES_MULTI ( bam_ch, bai_ch, genome_fasta, genome_fasta_fai )
 }
diff --git a/tests/modules/cnr-ibba/freebayes/single/main.nf b/tests/modules/cnr-ibba/freebayes/single/main.nf
@@ -20,8 +20,15 @@ workflow test_freebayes_single {
         file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
     ]
 
-    genome_fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    genome_fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    genome_fasta = [
+        [ id:'genome' ],
+        file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    ]
+
+    genome_fasta_fai = [
+        [ id:'genome' ],
+        file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    ]
 
     FREEBAYES_SINGLE ( input, BAMTOOLS_COVERAGE.out.data, genome_fasta, genome_fasta_fai, [] )
 }
diff --git a/tests/modules/cnr-ibba/freebayes/splitbam/main.nf b/tests/modules/cnr-ibba/freebayes/splitbam/main.nf
@@ -20,9 +20,15 @@ workflow test_freebayes_splitbam {
     bam_ch = Channel.of(bam).map{ it -> [[id: "all.fb"], it]}
     bai_ch = Channel.of(bai).map{ it -> [[id: "all.fb"], it]}
 
-    genome_fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    genome_fasta = [
+        [ id:'genome' ],
+        file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    ]
 
-    genome_fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    genome_fasta_fai = [
+        [ id:'genome' ],
+        file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    ]
 
     FREEBAYES_SPLITBAM ( bam_ch, bai_ch, genome_fasta, genome_fasta_fai )
 }
diff --git a/tests/subworkflows/cnr-ibba/freebayes_parallel/main.nf b/tests/subworkflows/cnr-ibba/freebayes_parallel/main.nf
@@ -19,9 +19,15 @@ workflow test_freebayes_parallel {
     bam_ch = Channel.of(bam).map{ it -> [[id: "all.fb"], it]}
     bai_ch = Channel.of(bai).map{ it -> [[id: "all.fb"], it]}
 
-    genome_fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    genome_fasta = [
+        [ id:'genome' ],
+        file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    ]
 
-    genome_fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    genome_fasta_fai = [
+        [ id:'genome' ],
+        file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    ]
 
     FREEBAYES_PARALLEL ( bam_ch, bai_ch, genome_fasta, genome_fasta_fai )
 }