Merge branch 'master' into krakentools/kreport2krona

modules/tiddit/sv/main.nf

@@ -2,10 +2,10 @@ process TIDDIT_SV {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::tiddit=3.0.0" : null)
+    conda (params.enable_conda ? "bioconda::tiddit=3.1.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/tiddit:3.0.0--py39h59fae87_1' :
-        'quay.io/biocontainers/tiddit:3.0.0--py39h59fae87_1' }"
+        'https://depot.galaxyproject.org/singularity/tiddit:3.1.0--py39h59fae87_1' :
+        'quay.io/biocontainers/tiddit:3.1.0--py39h59fae87_1' }"
 
     input:
     tuple val(meta), path(input), path(input_index)
@@ -23,8 +23,10 @@ process TIDDIT_SV {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def bwa_command = bwa_index ? "[[ -d $bwa_index ]] && for i in $bwa_index/*; do [[ -f $fasta && ! \"\$i\" =~ .*\"$fasta\".* ]] && ln -s \$i ${fasta}.\${i##*.} || ln -s \$i .; done" : ""
+
     """
-    [[ -d $bwa_index ]] && for i in $bwa_index/*; do [[ -f $fasta && ! "\$i" =~ .*"$fasta".* ]] && ln -s \$i ${fasta}.\${i##*.} || ln -s \$i .; done
+    $bwa_command
 
     tiddit \\
         --sv \\

tests/modules/tiddit/sv/main.nf

@@ -4,6 +4,7 @@ nextflow.enable.dsl = 2
 
 include { BWA_INDEX                    } from '../../../../modules/bwa/index/main.nf'
 include { TIDDIT_SV                    } from '../../../../modules/tiddit/sv/main.nf'
+include { TIDDIT_SV as TIDDIT_SV_NOBWA } from '../../../../modules/tiddit/sv/main.nf'
 
 workflow test_tiddit_sv_bam {
     input = [
@@ -32,3 +33,27 @@ workflow test_tiddit_sv_cram {
 
     TIDDIT_SV ( input, fasta, BWA_INDEX.out.index)
 }
+
+workflow test_tiddit_sv_nobwa_bam {
+    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_bai'], checkIfExists: true) ]
+    ]
+
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    TIDDIT_SV_NOBWA ( input, fasta, [])
+}
+
+workflow test_tiddit_sv_nobwa_cram {
+    input = [
+        [ id:'test' ], // meta map
+        [ 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) ]
+    ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+
+    TIDDIT_SV_NOBWA ( input, fasta, [])
+}

tests/modules/tiddit/sv/nextflow.config

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

tests/modules/tiddit/sv/test.yml

@@ -7,7 +7,7 @@
     - path: output/tiddit/test.ploidies.tab
       md5sum: 6319d3611f7b6b94425a184d274b3dfc
     - path: output/tiddit/test.vcf
-      md5sum: 41d3f8746f0420f894104321b7e64f67
+      md5sum: 157907671297c34bacfd3e73eff9bbdf
 
 - name: tiddit sv test_tiddit_sv_cram
   command: nextflow run ./tests/modules/tiddit/sv -entry test_tiddit_sv_cram -c ./tests/config/nextflow.config -c ./tests/modules/tiddit/sv/nextflow.config
@@ -18,4 +18,26 @@
     - path: output/tiddit/test.ploidies.tab
       md5sum: f1162a940ddc8b963f6e0e506bb5c136
     - path: output/tiddit/test.vcf
-      md5sum: 34db59578991285d6b62dc1500272fca
+      md5sum: 56687eeffa452f78f18d54a69dd17c78
+
+- name: tiddit sv test_tiddit_sv_nobwa_bam
+  command: nextflow run ./tests/modules/tiddit/sv -entry test_tiddit_sv_nobwa_bam -c ./tests/config/nextflow.config -c ./tests/modules/tiddit/sv/nextflow.config
+  tags:
+    - tiddit
+    - tiddit/sv
+  files:
+    - path: output/tiddit/test.ploidies.tab
+      md5sum: 6319d3611f7b6b94425a184d274b3dfc
+    - path: output/tiddit/test.vcf
+      md5sum: ddac94f9cd4f991b6ce2052d7f78a525
+
+- name: tiddit sv test_tiddit_sv_nobwa_cram
+  command: nextflow run ./tests/modules/tiddit/sv -entry test_tiddit_sv_nobwa_cram -c ./tests/config/nextflow.config -c ./tests/modules/tiddit/sv/nextflow.config
+  tags:
+    - tiddit
+    - tiddit/sv
+  files:
+    - path: output/tiddit/test.ploidies.tab
+      md5sum: f1162a940ddc8b963f6e0e506bb5c136
+    - path: output/tiddit/test.vcf
+      md5sum: 680e60574cc28d38c9673a916ecd675c