Merge branch 'master' into haplocheck

modules/tiddit/cov/main.nf

@@ -2,17 +2,17 @@ process TIDDIT_COV {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::tiddit=2.12.1" : null)
+    conda (params.enable_conda ? "bioconda::tiddit=3.0.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/tiddit:2.12.1--py38h1773678_0' :
+        'https://depot.galaxyproject.org/singularity/tiddit:3.0.0--py39h59fae87_1' :
-        'quay.io/biocontainers/tiddit:2.12.1--py38h1773678_0' }"
+        'quay.io/biocontainers/tiddit:3.0.0--py39h59fae87_1' }"
 
     input:
-    tuple val(meta), path(bam)
+    tuple val(meta), path(input)
     path  fasta
 
     output:
-    tuple val(meta), path("*.tab"), optional: true, emit: cov
+    tuple val(meta), path("*.bed"), optional: true, emit: cov
     tuple val(meta), path("*.wig"), optional: true, emit: wig
     path  "versions.yml"          , emit: versions
 
@@ -28,12 +28,12 @@ process TIDDIT_COV {
         --cov \\
         -o $prefix \\
         $args \\
-        --bam $bam \\
+        --bam $input \\
         $reference
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*TIDDIT-//; s/ .*\$//')
+        tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*tiddit-//; s/ .*\$//')
     END_VERSIONS
     """
 
@@ -45,7 +45,7 @@ process TIDDIT_COV {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*TIDDIT-//; s/ .*\$//')
+        tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*tiddit-//; s/ .*\$//')
     END_VERSIONS
     """
 }

modules/tiddit/cov/meta.yml

@@ -19,7 +19,7 @@ input:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  - bam:
+  - input:
       type: file
       description: BAM/CRAM file
       pattern: "*.{bam,cram}"

modules/tiddit/sv/main.nf

@@ -2,21 +2,20 @@ process TIDDIT_SV {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::tiddit=2.12.1" : null)
+    conda (params.enable_conda ? "bioconda::tiddit=3.0.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/tiddit:2.12.1--py38h1773678_0' :
+        'https://depot.galaxyproject.org/singularity/tiddit:3.0.0--py39h59fae87_1' :
-        'quay.io/biocontainers/tiddit:2.12.1--py38h1773678_0' }"
+        'quay.io/biocontainers/tiddit:3.0.0--py39h59fae87_1' }"
 
     input:
-    tuple val(meta), path(bam)
+    tuple val(meta), path(input), path(input_index)
     path  fasta
-    path  fai
+    path  bwa_index
 
     output:
-    tuple val(meta), path("*.vcf")        , emit: vcf
+    tuple val(meta), path("*.vcf")         , emit: vcf
-    tuple val(meta), path("*.ploidy.tab") , emit: ploidy
+    tuple val(meta), path("*.ploidies.tab"), emit: ploidy
-    tuple val(meta), path("*.signals.tab"), emit: signals
+    path  "versions.yml"                   , emit: versions
-    path  "versions.yml"                  , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -24,18 +23,19 @@ process TIDDIT_SV {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def reference = fasta ? "--ref $fasta" : ""
     """
+    [[ -d $bwa_index ]] && for i in $bwa_index/*; do [[ -f $fasta && ! "\$i" =~ .*"$fasta".* ]] && ln -s \$i ${fasta}.\${i##*.} || ln -s \$i .; done
+
     tiddit \\
         --sv \\
         $args \\
-        --bam $bam \\
+        --bam $input \\
-        $reference \\
+        --ref $fasta \\
         -o $prefix
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*TIDDIT-//; s/ .*\$//')
+        tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*tiddit-//; s/ .*\$//')
     END_VERSIONS
     """
 
@@ -43,12 +43,11 @@ process TIDDIT_SV {
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}.vcf
-    touch ${prefix}.ploidy.tab
+    touch ${prefix}.ploidies.tab
-    touch ${prefix}.signals.tab
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*TIDDIT-//; s/ .*\$//')
+        tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*tiddit-//; s/ .*\$//')
     END_VERSIONS
     """
 }

modules/tiddit/sv/meta.yml

@@ -17,14 +17,22 @@ input:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
+  - input:
+      type: file
+      description: BAM/CRAM file
+      pattern: "*.{bam,cram}"
+  - index:
+      type: file
+      description: BAM/CRAM index file
+      pattern: "*.{bai,crai}"
   - fasta:
       type: file
       description: Input FASTA file
       pattern: "*.{fasta,fa}"
-  - fai:
+  - bwa_index:
       type: file
-      description: FASTA index file
+      description: BWA genome index files
-      pattern: "*.{fai}"
+      pattern: "Directory containing BWA index *.{amb,ann,bwt,pac,sa}"
 output:
   - meta:
       type: map
@@ -38,11 +46,7 @@ output:
   - ploidy:
       type: file
       description: tab
-      pattern: "*.{ploidy.tab}"
+      pattern: "*.{ploidies.tab}"
-  - signals:
-      type: file
-      description: tab
-      pattern: "*.{signals.tab}"
   - versions:
       type: file
       description: File containing software versions

tests/modules/tiddit/cov/main.nf

@@ -2,22 +2,41 @@
 
 nextflow.enable.dsl = 2
 
-include { TIDDIT_COV } from '../../../../modules/tiddit/cov/main.nf'
+include { TIDDIT_COV as TIDDIT_COV_BED } from '../../../../modules/tiddit/cov/main.nf'
+include { TIDDIT_COV as TIDDIT_COV_WIG } from '../../../../modules/tiddit/cov/main.nf'
 
-workflow test_tiddit_cov {
+workflow test_tiddit_cov_cram_bed {
 
     input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
+            file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true) ]
 
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
 
-    TIDDIT_COV ( input, fasta )
+    TIDDIT_COV_BED ( input, fasta )
 }
 
-workflow test_tiddit_cov_no_ref {
+workflow test_tiddit_cov_bam_bed {
 
     input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
+            file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
 
-    TIDDIT_COV ( input, [] )
+    TIDDIT_COV_BED ( input, [] )
+}
+
+workflow test_tiddit_cov_cram_wig {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+            file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true) ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+
+    TIDDIT_COV_WIG ( input, fasta )
+}
+
+workflow test_tiddit_cov_bam_wig {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+            file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
+
+    TIDDIT_COV_WIG ( input, [] )
 }

tests/modules/tiddit/cov/nextflow.config

@@ -2,4 +2,8 @@ process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
 
+    withName: TIDDIT_COV_WIG {
+        ext.args = '-w'
+    }
+
 }

tests/modules/tiddit/cov/test.yml

@@ -1,17 +1,35 @@
-- name: tiddit cov test_tiddit_cov
+- name: tiddit cov test_tiddit_cov_cram_bed
-  command: nextflow run ./tests/modules/tiddit/cov -entry test_tiddit_cov -c ./tests/config/nextflow.config -c ./tests/modules/tiddit/cov/nextflow.config
+  command: nextflow run ./tests/modules/tiddit/cov -entry test_tiddit_cov_cram_bed -c ./tests/config/nextflow.config -c ./tests/modules/tiddit/cov/nextflow.config
   tags:
     - tiddit
     - tiddit/cov
   files:
-    - path: output/tiddit/test.tab
+    - path: output/tiddit/test.bed
-      md5sum: f7974948f809f94879d8a60b726194f5
+      md5sum: 3b1a28c62a5f25bbba77c1042e9abdf7
 
-- name: tiddit cov test_tiddit_cov_no_ref
+- name: tiddit cov test_tiddit_cov_bam_bed
-  command: nextflow run ./tests/modules/tiddit/cov -entry test_tiddit_cov_no_ref -c ./tests/config/nextflow.config -c ./tests/modules/tiddit/cov/nextflow.config
+  command: nextflow run ./tests/modules/tiddit/cov -entry test_tiddit_cov_bam_bed -c ./tests/config/nextflow.config -c ./tests/modules/tiddit/cov/nextflow.config
   tags:
     - tiddit
     - tiddit/cov
   files:
-    - path: output/tiddit/test.tab
+    - path: output/tiddit/test.bed
-      md5sum: f7974948f809f94879d8a60b726194f5
+      md5sum: 9d1474f1c7c6516205254077087bb026
+
+- name: tiddit cov test_tiddit_cov_cram_wig
+  command: nextflow run ./tests/modules/tiddit/cov -entry test_tiddit_cov_cram_wig -c ./tests/config/nextflow.config -c ./tests/modules/tiddit/cov/nextflow.config
+  tags:
+    - tiddit
+    - tiddit/cov
+  files:
+    - path: output/tiddit/test.wig
+      md5sum: ca3645fd0c3491c86c075c91d16d57c4
+
+- name: tiddit cov test_tiddit_cov_bam_wig
+  command: nextflow run ./tests/modules/tiddit/cov -entry test_tiddit_cov_bam_wig -c ./tests/config/nextflow.config -c ./tests/modules/tiddit/cov/nextflow.config
+  tags:
+    - tiddit
+    - tiddit/cov
+  files:
+    - path: output/tiddit/test.wig
+      md5sum: 44bea2ac6a56774738e65773065da670

tests/modules/tiddit/sv/main.nf

@@ -2,25 +2,33 @@
 
 nextflow.enable.dsl = 2
 
+include { BWA_INDEX } from '../../../../modules/bwa/index/main.nf'
 include { TIDDIT_SV } from '../../../../modules/tiddit/sv/main.nf'
 
-workflow test_tiddit_sv {
+workflow test_tiddit_sv_bam {
-    input = [ 
+    input = [
         [ id:'test' ], // meta map
-        [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ] 
+        [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ],
+        [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ]
     ]
-    
+
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
 
-    TIDDIT_SV ( input, fasta, fai )
+    BWA_INDEX( fasta )
+
+    TIDDIT_SV ( input, fasta, BWA_INDEX.out.index)
 }
 
-workflow test_tiddit_sv_no_ref {
+workflow test_tiddit_sv_cram {
-    input = [ 
+    input = [
         [ id:'test' ], // meta map
-        [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ] 
+        [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true) ],
+        [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true) ]
     ]
 
-    TIDDIT_SV ( input, [], [] )
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+
+    BWA_INDEX( fasta )
+
+    TIDDIT_SV ( input, fasta, BWA_INDEX.out.index)
 }

tests/modules/tiddit/sv/test.yml

@@ -1,25 +1,21 @@
-- name: tiddit sv
+- name: tiddit sv test_tiddit_sv_bam
-  command: nextflow run ./tests/modules/tiddit/sv -entry test_tiddit_sv -c ./tests/config/nextflow.config -c ./tests/modules/tiddit/sv/nextflow.config
+  command: nextflow run ./tests/modules/tiddit/sv -entry test_tiddit_sv_bam -c ./tests/config/nextflow.config -c ./tests/modules/tiddit/sv/nextflow.config
   tags:
     - tiddit
     - tiddit/sv
   files:
-    - path: output/tiddit/test.ploidy.tab
+    - path: output/tiddit/test.ploidies.tab
-      md5sum: 45e050b0e204f0a5a3a99627cc440eaa
+      md5sum: 6319d3611f7b6b94425a184d274b3dfc
-    - path: output/tiddit/test.signals.tab
-      md5sum: dab4b2fec4ddf8eb1c23005b0770150e
     - path: output/tiddit/test.vcf
-      md5sum: bdce14ae8292bf3deb81f6f255baf859
+      md5sum: 41d3f8746f0420f894104321b7e64f67
 
-- name: tiddit sv no ref
+- name: tiddit sv test_tiddit_sv_cram
-  command: nextflow run ./tests/modules/tiddit/sv -entry test_tiddit_sv_no_ref -c ./tests/config/nextflow.config -c ./tests/modules/tiddit/sv/nextflow.config
+  command: nextflow run ./tests/modules/tiddit/sv -entry test_tiddit_sv_cram -c ./tests/config/nextflow.config -c ./tests/modules/tiddit/sv/nextflow.config
   tags:
     - tiddit
     - tiddit/sv
   files:
-    - path: output/tiddit/test.ploidy.tab
+    - path: output/tiddit/test.ploidies.tab
-      md5sum: 45e050b0e204f0a5a3a99627cc440eaa
+      md5sum: f1162a940ddc8b963f6e0e506bb5c136
-    - path: output/tiddit/test.signals.tab
-      md5sum: dab4b2fec4ddf8eb1c23005b0770150e
     - path: output/tiddit/test.vcf
-      md5sum: 3d0e83a8199b2bdb81cfe3e6b12bf64b
+      md5sum: 34db59578991285d6b62dc1500272fca