From b689b8ed88a9f89eb2f7c75d3eb0bace77ade109 Mon Sep 17 00:00:00 2001
From: "Maxime U. Garcia" <max.u.garcia@gmail.com>
Date: Mon, 13 Jun 2022 17:02:59 +0200
Subject: [PATCH] TIDDIT - add --skip_assembly when no bwa specified (#1769)

add --skip_assembly when no bwa specified
---
 modules/tiddit/sv/main.nf               |  4 +++-
 tests/modules/tiddit/sv/main.nf         | 29 +++++++++++++++++++++++--
 tests/modules/tiddit/sv/nextflow.config |  4 ++++
 tests/modules/tiddit/sv/test.yml        | 22 +++++++++++++++++++
 4 files changed, 56 insertions(+), 3 deletions(-)

diff --git a/modules/tiddit/sv/main.nf b/modules/tiddit/sv/main.nf
index 2622963c..2e876ef1 100644
--- a/modules/tiddit/sv/main.nf
+++ b/modules/tiddit/sv/main.nf
@@ -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 \\
diff --git a/tests/modules/tiddit/sv/main.nf b/tests/modules/tiddit/sv/main.nf
index c9dbf4ea..2f944129 100644
--- a/tests/modules/tiddit/sv/main.nf
+++ b/tests/modules/tiddit/sv/main.nf
@@ -2,8 +2,9 @@
 
 nextflow.enable.dsl = 2
 
-include { BWA_INDEX } from '../../../../modules/bwa/index/main.nf'
-include { TIDDIT_SV } from '../../../../modules/tiddit/sv/main.nf'
+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, [])
+}
diff --git a/tests/modules/tiddit/sv/nextflow.config b/tests/modules/tiddit/sv/nextflow.config
index 8730f1c4..d9a85fd3 100644
--- a/tests/modules/tiddit/sv/nextflow.config
+++ b/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'
+    }
+
 }
diff --git a/tests/modules/tiddit/sv/test.yml b/tests/modules/tiddit/sv/test.yml
index dbc8e353..5bbfe4ae 100644
--- a/tests/modules/tiddit/sv/test.yml
+++ b/tests/modules/tiddit/sv/test.yml
@@ -19,3 +19,25 @@
       md5sum: f1162a940ddc8b963f6e0e506bb5c136
     - path: output/tiddit/test.vcf
       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