Remove bcftools and ivar module customisations (#1217)

* Remove customisation from bcftools modules

* Add save_mpileup option to bcftools/mpileup

* Remove params.save_mpileup from ivar/consensus

* Update meta.ymls

modules/bcftools/consensus/main.nf

@@ -18,9 +18,12 @@ process BCFTOOLS_CONSENSUS {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    cat $fasta | bcftools consensus $vcf $args > ${prefix}.fa
-    header=\$(head -n 1 ${prefix}.fa | sed 's/>//g')
-    sed -i 's/\${header}/${meta.id}/g' ${prefix}.fa
+    cat $fasta \\
+        | bcftools \\
+            consensus \\
+            $vcf \\
+            $args \\
+            > ${prefix}.fa
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/bcftools/mpileup/main.nf

@@ -10,11 +10,13 @@ process BCFTOOLS_MPILEUP {
     input:
     tuple val(meta), path(bam)
     path fasta
+    val save_mpileup
 
     output:
     tuple val(meta), path("*.gz")      , emit: vcf
     tuple val(meta), path("*.tbi")     , emit: tbi
     tuple val(meta), path("*stats.txt"), emit: stats
+    tuple val(meta), path("*.mpileup") , emit: mpileup, optional: true
     path  "versions.yml"               , emit: versions
 
     script:
@@ -22,13 +24,16 @@ process BCFTOOLS_MPILEUP {
     def args2 = task.ext.args2 ?: ''
     def args3 = task.ext.args3 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def mpileup = save_mpileup ? "| tee ${prefix}.mpileup" : ""
     """
     echo "${meta.id}" > sample_name.list
 
-    bcftools mpileup \\
+    bcftools \\
+        mpileup \\
         --fasta-ref $fasta \\
         $args \\
         $bam \\
+        $mpileup \\
         | bcftools call --output-type v $args2 \\
         | bcftools reheader --samples sample_name.list \\
         | bcftools view --output-file ${prefix}.vcf.gz --output-type z $args3

modules/bcftools/mpileup/meta.yml

@@ -26,6 +26,10 @@ input:
         type: file
         description: FASTA reference file
         pattern: "*.{fasta,fa}"
+    - save_mpileup:
+        type: boolean
+        description: Save mpileup file generated by bcftools mpileup
+        patter: "*.mpileup"
 output:
     - meta:
         type: map

modules/ivar/consensus/main.nf

@@ -10,6 +10,7 @@ process IVAR_CONSENSUS {
     input:
     tuple val(meta), path(bam)
     path fasta
+    val save_mpileup
 
     output:
     tuple val(meta), path("*.fa")      , emit: fasta
@@ -21,14 +22,16 @@ process IVAR_CONSENSUS {
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def save_mpileup = params.save_mpileup ? "tee ${prefix}.mpileup |" : ""
+    def mpileup = save_mpileup ? "| tee ${prefix}.mpileup" : ""
     """
-    samtools mpileup \\
+    samtools \\
+        mpileup \\
         --reference $fasta \\
         $args2 \\
-        $bam | \\
-        $save_mpileup \\
-        ivar consensus \\
+        $bam \\
+        $mpileup \\
+        | ivar \\
+            consensus \\
             $args \\
             -p $prefix
 

modules/ivar/consensus/meta.yml

@@ -25,6 +25,10 @@ input:
         type: file
         description: The reference sequence used for mapping and generating the BAM file
         pattern: "*.fa"
+    - save_mpileup:
+        type: boolean
+        description: Save mpileup file generated by ivar consensus
+        patter: "*.mpileup"
 output:
     - meta:
         type: map

modules/ivar/variants/main.nf

@@ -23,14 +23,16 @@ process IVAR_VARIANTS {
     def args2 = task.ext.args2 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def features = gff ? "-g $gff" : ""
-    def mpileup = save_mpileup ? "tee ${prefix}.mpileup |" : ""
+    def mpileup = save_mpileup ? "| tee ${prefix}.mpileup" : ""
     """
-    samtools mpileup \\
+    samtools \\
+        mpileup \\
         $args2 \\
         --reference $fasta \\
-        $bam | \\
+        $bam \\
         $mpileup \\
-        ivar variants \\
+        | ivar \\
+            variants \\
             $args \\
             $features \\
             -r $fasta \\

modules/ivar/variants/meta.yml

@@ -32,6 +32,7 @@ input:
     - save_mpileup:
         type: boolean
         description: Save mpileup file generated by ivar variants
+        patter: "*.mpileup"
 output:
     - meta:
         type: map

tests/modules/bcftools/consensus/main.nf

@@ -5,10 +5,12 @@ nextflow.enable.dsl = 2
 include { BCFTOOLS_CONSENSUS } from '../../../../modules/bcftools/consensus/main.nf'
 
 workflow test_bcftools_consensus {
-    input = [ [ id:'test' ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) ],
-              [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true) ],
-              [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+
+    input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
+        file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true),
+        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
     ]
 
     BCFTOOLS_CONSENSUS ( input )

tests/modules/bcftools/mpileup/main.nf

@@ -5,9 +5,25 @@ nextflow.enable.dsl = 2
 include { BCFTOOLS_MPILEUP } from '../../../../modules/bcftools/mpileup/main.nf'
 
 workflow test_bcftools_mpileup {
-    input = [ [ id:'test' ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]]
-    fasta = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
 
-    BCFTOOLS_MPILEUP ( input, fasta )
+    input = [
+        [ id:'test' ], // meta map
+        [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    save_mpileup = false
+
+    BCFTOOLS_MPILEUP ( input, fasta, save_mpileup )
+}
+
+workflow test_bcftools_save_mpileup {
+
+    input = [
+        [ id:'test' ], // meta map
+        [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    save_mpileup = true
+
+    BCFTOOLS_MPILEUP ( input, fasta, save_mpileup )
 }

tests/modules/bcftools/mpileup/test.yml

@@ -10,3 +10,18 @@
       md5sum: ae0f17dcc2cb27034d848699b824c516
     - path: output/bcftools/test.vcf.gz
       md5sum: e9e520663875c66296f3bff0fa226c40
+
+- name: bcftools mpileup test_bcftools_save_mpileup
+  command: nextflow run ./tests/modules/bcftools/mpileup -entry test_bcftools_save_mpileup -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/mpileup/nextflow.config
+  tags:
+    - bcftools/mpileup
+    - bcftools
+  files:
+    - path: output/bcftools/test.bcftools_stats.txt
+      md5sum: 72c506e633413c6b439f95336933984e
+    - path: output/bcftools/test.vcf.gz.tbi
+      md5sum: ae0f17dcc2cb27034d848699b824c516
+    - path: output/bcftools/test.vcf.gz
+      md5sum: e9e520663875c66296f3bff0fa226c40
+    - path: output/bcftools/test.mpileup
+      md5sum: fe0e45a57ffdfb253ed6794f8356a3f0

tests/modules/ivar/consensus/main.nf

@@ -2,14 +2,28 @@
 
 nextflow.enable.dsl = 2
 
-params.save_mpileup = true
 include { IVAR_CONSENSUS } from '../../../../modules/ivar/consensus/main.nf'
 
 workflow test_ivar_consensus {
-    input = [ [ id:'test'],
+
+    input = [
+        [ id:'test'],
         file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
     ]
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    save_mpileup = false
 
-    IVAR_CONSENSUS ( input, fasta )
+    IVAR_CONSENSUS ( input, fasta, save_mpileup)
+}
+
+workflow test_ivar_consensus_mpileup {
+
+    input = [
+        [ id:'test'],
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    save_mpileup = true
+
+    IVAR_CONSENSUS ( input, fasta, save_mpileup)
 }

tests/modules/ivar/consensus/test.yml

@@ -1,5 +1,16 @@
-- name: ivar consensus
+- name: ivar consensus test_ivar_consensus
   command: nextflow run ./tests/modules/ivar/consensus -entry test_ivar_consensus -c ./tests/config/nextflow.config -c ./tests/modules/ivar/consensus/nextflow.config
+  tags:
+    - ivar
+    - ivar/consensus
+  files:
+    - path: output/ivar/test.fa
+      md5sum: 9e21a64818f4302b4dece5480fa5e8b8
+    - path: output/ivar/test.qual.txt
+      md5sum: 68b329da9893e34099c7d8ad5cb9c940
+
+- name: ivar consensus test_ivar_consensus_mpileup
+  command: nextflow run ./tests/modules/ivar/consensus -entry test_ivar_consensus_mpileup -c ./tests/config/nextflow.config -c ./tests/modules/ivar/consensus/nextflow.config
   tags:
     - ivar
     - ivar/consensus