add saltshaker modules

CITATIONS.md

@@ -82,6 +82,10 @@
 
   > Chen X, Schulz-Trieglaff O, Shaw R, et al. Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications. Bioinformatics. 2016;32(8):1220-1222. doi:10.1093/bioinformatics/btv710
 
+- [Mitosalt](https://sourceforge.net/projects/mitosalt/)
+
+  > Basu S, Xie X, Uhler JP, et al. Accurate mapping of mitochondrial DNA deletions and duplications using deep sequencing. PLoS Genet. 2020;16(12):e1009242. doi: 10.1371/journal.pgen.1009242
+
 - [Mosdepth](https://academic.oup.com/bioinformatics/article/34/5/867/4583630?login=true)
 
   > Pedersen BS, Quinlan AR. Mosdepth: quick coverage calculation for genomes and exomes. Hancock J, ed. Bioinformatics. 2018;34(5):867-868. doi:10.1093/bioinformatics/btx699
@@ -112,6 +116,8 @@
 
   > John G. Cleary, Ross Braithwaite, Kurt Gaastra, Brian S. Hilbush, Stuart Inglis, Sean A. Irvine, Alan Jackson, Richard Littin, Mehul Rathod, David Ware, Justin M. Zook, Len Trigg, and Francisco M. De La Vega. "Comparing Variant Call Files for Performance Benchmarking of Next-Generation Sequencing Variant Calling Pipelines." bioRxiv, 2015. doi:10.1101/023754.
 
+- [saltshaker](https://pypi.org/project/saltshaker/)
+
 - [Sambamba](https://academic.oup.com/bioinformatics/article/31/12/2032/213831)
 
   > Tarasov A, Vilella AJ, Cuppen E, Nijman IJ, Prins P. Sambamba: fast processing of NGS alignment formats. Bioinformatics. 2015;31(12):2032-2034. doi:10.1093/bioinformatics/btv098

conf/modules/call_sv_MT.config

@@ -22,4 +22,19 @@ process {
         ext.prefix = { "${meta.id}_mitochondria_deletions" }
     }
 
+    withName: '.*CALL_SV_MT:SALTSHAKER_CALL' {
+        ext.args = '--blacklist'
+    }
+
+    withName: '.*CALL_SV_MT:SALTSHAKER_CLASSIFY' {
+        ext.args = { "--blacklist --vcf --dominant-fraction ${params.saltshaker_dominant_fraction} \
+            --radius ${params.saltshaker_group_radius} --high-het ${params.saltshaker_high_heteroplasmy} \
+            --multiple-threshold ${params.saltshaker_multiple_threshold} --noise ${params.saltshaker_noise_threshold}"
+        }
+    }
+
+    withName: '.*CALL_SV_MT:SALTSHAKER_PLOT' {
+        ext.args = '--blacklist --genes'
+    }
+
 }

conf/test.config

@@ -22,8 +22,6 @@ env {
     MPLCONFIGDIR="."
 }
 
-singularity.pullTimeout='2h'
-
 params {
     config_profile_name             = 'Test profile - default'
     config_profile_description      = 'Minimal test dataset to check pipeline function'

main.nf

@@ -316,13 +316,17 @@ workflow NFCORE_RAREDISEASE {
     //
     if (skip_germlinecnvcaller) {
         if (val_analysis_type.equals("wgs")) {
-            ch_svcaller_priority = channel.value(["tiddit", "manta", "cnvnator"])
+            ch_svcaller_priority = channel.value(["tiddit", "manta", "cnvnator", "mitosalt"])
+        } else if (val_run_mt_for_wes) {
+            ch_svcaller_priority = channel.value(["mitosalt"])
         } else {
             ch_svcaller_priority = channel.value([])
         }
     } else {
         if (val_analysis_type.equals("wgs")) {
-            ch_svcaller_priority = channel.value(["tiddit", "manta", "gcnvcaller", "cnvnator"])
+            ch_svcaller_priority = channel.value(["tiddit", "manta", "gcnvcaller", "cnvnator", "mitosalt"])
+        } else if (val_run_mt_for_wes) {
+            ch_svcaller_priority = channel.value(["manta", "gcnvcaller", "mitosalt"])        
         } else {
             ch_svcaller_priority = channel.value(["manta", "gcnvcaller"])
         }

modules.json

@@ -396,6 +396,21 @@
                         "git_sha": "0f04646a9282049b16b3eb35b042e94dfb3340a0",
                         "installed_by": ["modules"]
                     },
+                    "saltshaker/call": {
+                        "branch": "master",
+                        "git_sha": "9d051963759dda1a424374e23f4f22aaa2b0bd60",
+                        "installed_by": ["modules"]
+                    },
+                    "saltshaker/classify": {
+                        "branch": "master",
+                        "git_sha": "ff5f2ad4481a4a1e1769a1fad922681e7f7fd176",
+                        "installed_by": ["modules"]
+                    },
+                    "saltshaker/plot": {
+                        "branch": "master",
+                        "git_sha": "ff5f2ad4481a4a1e1769a1fad922681e7f7fd176",
+                        "installed_by": ["modules"]
+                    },
                     "sambamba/depth": {
                         "branch": "master",
                         "git_sha": "ca6da11b05740de461b1e2714037345c0f856201",

modules/local/mitosalt/main.nf

@@ -4,9 +4,8 @@ process MITOSALT {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/dc/dc2631dac526622d28ea1109b0f714d536606d0e5b3b85fe24407c8206e7e6b6/data':
-        'community.wave.seqera.io/library/mitosalt:1.1.1--5fd87ac48a683358' }"
-
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/13/130779a0dd5a8d86441f262a16a5fb1dfe562125edf93646b53c893d982b5519/data':
+        'community.wave.seqera.io/library/bbmap_bedtools_bioconductor-biostrings_bioconductor-pwalign_pruned:856c05081cbd8239' }"
 
     input:
     tuple val(meta), path(reads)
@@ -28,7 +27,7 @@ process MITOSALT {
     """
     cat $msconfig | sed "s/threads = 1/threads = ${task.cpus}/" > new-${msconfig}
     mkdir -p log indel bam tab bw plot
-    mitosalt new-${msconfig} $reads $prefix
+    MitoSAlt1.1.1.pl new-${msconfig} $reads $prefix
     mv indel/*.breakpoint ${prefix}.breakpoint
     mv indel/*.cluster ${prefix}.cluster
     """
@@ -38,7 +37,7 @@ process MITOSALT {
     """
     cat $msconfig | sed "s/threads = 1/threads = ${task.cpus}/" > new-${msconfig}
     touch ${prefix}.breakpoint
-    touch ${prefix}.cluster
+    echo 'cluster' > ${prefix}.cluster
     """
 
 }

modules/local/mitosalt/resources/usr/bin/MitoSAlt1.1.1.pl

@@ -10,14 +10,6 @@
 my $p2 = $ARGV[2];
 my $tag = $ARGV[3];
 
-#CREATE DIRECTORIES -- added by ID
-mkdir "log" unless -d "log";
-mkdir "indel" unless -d "indel";
-mkdir "bam" unless -d "bam";
-mkdir "tab" unless -d "tab";
-mkdir "bw" unless -d "bw";
-mkdir "plot" unless -d "plot";
-
 #LOG
 open (STDOUT, "| tee -ai log/$tag.log");
 
@@ -158,7 +150,7 @@
 if($nu_mt eq 'no' && $o_mt eq 'yes' && $enriched eq 'yes'){
   #REMAP ON MT GENOME
   print scalar(localtime).": Map to MT genome\n";
-  system("$reformat in=$p1 in2=$p2 out=tmp_$tag.fq overwrite=true addslash=t trimreaddescription=t spaceslash=f -Xmx100g"); #2>> log/$tag.log");
+  system("$reformat in=$p1 in2=$p2 out=tmp_$tag.fq overwrite=true addslash=t trimreaddescription=t spaceslash=f -Xmx100g 2>> log/$tag.log");
   system("$lastal -Q1 -e80 -P$threads $lastindex tmp_$tag.fq|$lastsp > tmp_$tag.maf");
   system("$mfcv sam -d tmp_$tag.maf|$samtools view -@ $threads -bt $mtfaindex -|$samtools sort -@ $threads -o bam/$tag.bam -");
   system("$samtools index bam/$tag.bam");

modules/local/prep_mitosalt/main.nf

@@ -53,6 +53,7 @@ process PREP_MITOSALT {
     echo "MT_fasta = ${mtfasta}"                                  >> mitosalt_config.txt
     echo "threads = 1"                                            >> mitosalt_config.txt
     echo "refchr = ${mito_name}"                                  >> mitosalt_config.txt
+    echo "msize = 16569"                                          >> mitosalt_config.txt
     echo "exclude = ${exclude}"                                   >> mitosalt_config.txt
     echo "orihs = 16081"                                          >> mitosalt_config.txt
     echo "orihe = 407"                                            >> mitosalt_config.txt