From 97e66015caec35f7fd6d095b9fc797549fee9efc Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Fri, 3 Jun 2022 15:51:02 +0200
Subject: [PATCH] add test + fix issues

---
 modules/tiddit/sv/main.nf        |  7 ++-----
 modules/tiddit/sv/meta.yml       | 20 ++++++++++++--------
 tests/modules/tiddit/sv/main.nf  | 17 +++++++++++++++--
 tests/modules/tiddit/sv/test.yml | 11 +++++++++++
 4 files changed, 40 insertions(+), 15 deletions(-)

diff --git a/modules/tiddit/sv/main.nf b/modules/tiddit/sv/main.nf
index 712f364b..ee2a8d75 100644
--- a/modules/tiddit/sv/main.nf
+++ b/modules/tiddit/sv/main.nf
@@ -10,7 +10,6 @@ process TIDDIT_SV {
     input:
     tuple val(meta), path(input), path(index)
     path  fasta
-    path  fai
     path  bwa_index
 
     output:
@@ -24,7 +23,6 @@ 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 `ls $bwa_index`; do [[ -f $fasta && ! "\$i" =~ .*"$fasta".* ]] && ln -s $bwa_index/\$i ${fasta}.\${i##*.} || ln -s $bwa_index/\$i \$i; done
 
@@ -32,7 +30,7 @@ process TIDDIT_SV {
         --sv \\
         $args \\
         --bam $input \\
-        $reference \\
+        --ref $fasta \\
         -o $prefix
 
     cat <<-END_VERSIONS > versions.yml
@@ -45,8 +43,7 @@ process TIDDIT_SV {
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}.vcf
-    touch ${prefix}.ploidy.tab
-    touch ${prefix}.signals.tab
+    touch ${prefix}.ploidies.tab
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/tiddit/sv/meta.yml b/modules/tiddit/sv/meta.yml
index fc307081..8b41c69c 100644
--- a/modules/tiddit/sv/meta.yml
+++ b/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
-      pattern: "*.{fai}"
+      description: BWA genome index files
+      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}"
-  - signals:
-      type: file
-      description: tab
-      pattern: "*.{signals.tab}"
+      pattern: "*.{ploidies.tab}"
   - versions:
       type: file
       description: File containing software versions
diff --git a/tests/modules/tiddit/sv/main.nf b/tests/modules/tiddit/sv/main.nf
index 2c09404e..c9dbf4ea 100644
--- a/tests/modules/tiddit/sv/main.nf
+++ b/tests/modules/tiddit/sv/main.nf
@@ -13,9 +13,22 @@ workflow test_tiddit_sv_bam {
     ]
 
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
 
     BWA_INDEX( fasta )
 
-    TIDDIT_SV ( input, fasta, fai , BWA_INDEX.out.index)
+    TIDDIT_SV ( input, fasta, BWA_INDEX.out.index)
+}
+
+workflow test_tiddit_sv_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)
+
+    BWA_INDEX( fasta )
+
+    TIDDIT_SV ( input, fasta, BWA_INDEX.out.index)
 }
diff --git a/tests/modules/tiddit/sv/test.yml b/tests/modules/tiddit/sv/test.yml
index 732b8434..557a0913 100644
--- a/tests/modules/tiddit/sv/test.yml
+++ b/tests/modules/tiddit/sv/test.yml
@@ -8,3 +8,14 @@
       md5sum: 6319d3611f7b6b94425a184d274b3dfc
     - path: output/tiddit/test.vcf
       md5sum: 41d3f8746f0420f894104321b7e64f67
+
+- 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
+  tags:
+    - tiddit
+    - tiddit/sv
+  files:
+    - path: output/tiddit/test.ploidies.tab
+      md5sum: f1162a940ddc8b963f6e0e506bb5c136
+    - path: output/tiddit/test.vcf
+      md5sum: 34db59578991285d6b62dc1500272fca