restructure tiddit/sv + test (just one for now)

modules/tiddit/sv/main.nf

@@ -8,16 +8,15 @@ process TIDDIT_SV {
         'quay.io/biocontainers/tiddit:3.0.0--py39h59fae87_1' }"
 
     input:
-    tuple val(meta), path(input)
+    tuple val(meta), path(input), path(index)
     path  fasta
     path  fai
     path  bwa_index
 
     output:
-    tuple val(meta), path("*.vcf")        , emit: vcf
-    tuple val(meta), path("*.ploidy.tab") , emit: ploidy
-    tuple val(meta), path("*.signals.tab"), emit: signals
-    path  "versions.yml"                  , emit: versions
+    tuple val(meta), path("*.vcf")         , emit: vcf
+    tuple val(meta), path("*.ploidies.tab"), emit: ploidy
+    path  "versions.yml"                   , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -27,7 +26,11 @@ process TIDDIT_SV {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def reference = fasta ? "--ref $fasta" : ""
     """
-    INDEX=`find -L ./ -name "*.amb" | sed 's/.amb//'`
+    for i in `ls ${bwa_index}`
+    do
+        ln -s ${bwa_index}/\$i ${fasta}.\${i##*.}
+    done
+
 
     tiddit \\
         --sv \\
@@ -38,7 +41,7 @@ process TIDDIT_SV {
 
     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
     """
 
@@ -51,7 +54,7 @@ process TIDDIT_SV {
 
     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
     """
 }

tests/modules/tiddit/sv/main.nf

@@ -5,10 +5,11 @@ 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 = [
         [ 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)
@@ -18,24 +19,3 @@ workflow test_tiddit_sv {
 
     TIDDIT_SV ( input, fasta, fai , BWA_INDEX.out.index)
 }
-
-workflow test_tiddit_sv_no_ref {
-    input = [
-        [ id:'test' ], // meta map
-        [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
-    ]
-
-    TIDDIT_SV ( input, [], [] )
-}
-
-workflow test_tiddit_sv_cram {
-    input = [
-        [ id:'test' ], // 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)
-    fai   = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-
-    TIDDIT_SV ( input, fasta, fai )
-}

tests/modules/tiddit/sv/test.yml

@@ -1,25 +1,10 @@
-- name: tiddit sv
-  command: nextflow run ./tests/modules/tiddit/sv -entry test_tiddit_sv -c ./tests/config/nextflow.config -c ./tests/modules/tiddit/sv/nextflow.config
+- name: tiddit sv test_tiddit_sv_bam
+  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
-      md5sum: 45e050b0e204f0a5a3a99627cc440eaa
-    - path: output/tiddit/test.signals.tab
-      md5sum: dab4b2fec4ddf8eb1c23005b0770150e
+    - path: output/tiddit/test.ploidies.tab
+      md5sum: 6319d3611f7b6b94425a184d274b3dfc
     - path: output/tiddit/test.vcf
-      md5sum: bdce14ae8292bf3deb81f6f255baf859
-
-- name: tiddit sv no ref
-  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
-  tags:
-    - tiddit
-    - tiddit/sv
-  files:
-    - path: output/tiddit/test.ploidy.tab
-      md5sum: 45e050b0e204f0a5a3a99627cc440eaa
-    - path: output/tiddit/test.signals.tab
-      md5sum: dab4b2fec4ddf8eb1c23005b0770150e
-    - path: output/tiddit/test.vcf
-      md5sum: 3d0e83a8199b2bdb81cfe3e6b12bf64b
+      md5sum: 41d3f8746f0420f894104321b7e64f67