From 88286d01c90baddf6f17ca6e4fb1f36bc7b6556a Mon Sep 17 00:00:00 2001
From: Gianpaolo <bitrix@hotmail.it>
Date: Fri, 14 Jan 2022 01:45:43 +0000
Subject: [PATCH 1/7] storedir applied

---
 pipeline.nf | 116 ++++++++++++++++++++++++++--------------------------
 1 file changed, 58 insertions(+), 58 deletions(-)

diff --git a/pipeline.nf b/pipeline.nf
index 7a1c570..7e41ffb 100644
--- a/pipeline.nf
+++ b/pipeline.nf
@@ -39,7 +39,7 @@ def helpMessage() {
 
     Other options:
       --outdir [dir]                  The output directory where the results will be saved
-      
+
     """.stripIndent()
 }
 
@@ -55,7 +55,7 @@ if (params.help) {
     exit 0
 }
 
-// Files and folders set up from default directories or directories defined in command line 
+// Files and folders set up from default directories or directories defined in command line
 refDir_refgen = file(params.referenceGenome)
 refDir_refgen_index = file(params.referenceGenome_index)
 
@@ -80,16 +80,16 @@ params.skip_genefuse = refDir_genefuse.exists()
 // INTEGRATE variables set up (this variable could be modified, for this reason they cannot be defined in the configuration file)
 integrateWGSt = false
 integrateWGSn = false
-command1 = "" 
-command2 = "" 
+command1 = ""
+command2 = ""
 
 // If the user inserts DNA data in the command line the INTEGRATE variable are modified
-if (params.dnareads_tumor) { 
+if (params.dnareads_tumor) {
   integrateWGSt = true
   command1 = "dna.tumor.bam"
 }
 
-if (params.dnareads_normal) { 
+if (params.dnareads_normal) {
   integrateWGSn = true
   command2 = "dna.normal.bam"
 }
@@ -129,12 +129,12 @@ Channel.fromPath(params.genefuse_ref).set{ input_ch1_genefuse }
 (refgen_downloader , refgen_integrate , refgen_integrate_builder, refgen_integrate_converter, refgen_genefuse, refgen_referenceGenome_index) = ( params.skip_refgen ? [Channel.empty(), input_ch1_refgen, input_ch2_refgen, input_ch3_refgen, input_ch4_refgen, input_ch5_refgen] : [input_ch1_refgen, Channel.empty(), Channel.empty(), Channel.empty(), Channel.empty(), Channel.empty()] )
 (refgen_index_trigger , refgen_index) = ( (params.skip_refgen_index || params.dnabam) ? [Channel.empty(), input_ch1_refgen_index] : [input_ch1_refgen_index, Channel.empty()] )
 
-(ch1_ericscript, ch2_ericscript) = ( params.skip_ericscript ? [Channel.empty(), input_ch_ericscript] : [input_ch_ericscript, Channel.empty()] )
+(ch1_ericscript, ch2_ericscript) =  [input_ch_ericscript, Channel.empty()]
 (ch1_arriba, ch2_arriba) = ( params.skip_arriba ? [Channel.empty(), input_ch_arriba] : [input_ch_arriba, Channel.empty()] )
 (ch1_fusioncatcher , ch2_fusioncatcher) = ( params.skip_fusioncatcher ? [Channel.empty(), input_ch_fusioncatcher] : [input_ch_fusioncatcher, Channel.empty()] )
 (ch1_integrate , ch2_integrate , ch3_integrate, ch4_integrate) = ( params.skip_integrate ? [Channel.empty(), input_ch1_integrate, input_ch2_integrate, input_ch3_integrate] : [input_ch1_integrate, Channel.empty(), Channel.empty(), Channel.empty()] )
 (ch1_integrate_bwts , ch2_integrate_bwts) = ( params.skip_integrate_bulder ? [Channel.empty(), input_ch1_bwts] : [input_ch1_bwts, Channel.empty()] )
-(ch1_genefuse , ch2_genefuse ) = ( params.skip_genefuse ? [Channel.empty(), input_ch1_genefuse] : [input_ch1_genefuse, Channel.empty()] )
+(ch1_genefuse , ch2_genefuse ) = [input_ch1_genefuse, Channel.empty()]
 
 /*
  * Reference Genome
@@ -145,14 +145,14 @@ process referenceGenome_downloader{
     tag "Downloading"
 
     // publishDir publishes the output in a specific folder with copy mode
-    publishDir "${params.outdir}/reference_genome", mode: 'copy'
-    
+    storeDir "${params.outdir}/reference_genome"
+
     input:
     val trigger from refgen_downloader
 
     output:
     file "hg38.fa" into refgen_integrate_builder_down, refgen_integrate_converter_down, refgen_referenceGenome_index_down, refgen_integrate_down, refgen_genefuse_down
-    
+
     // Conditions for the process execution
     when: params.integrate || params.genefuse || !(params.arriba || params.ericscript || params.fusioncatcher || params.genefuse || params.integrate)
 
@@ -173,7 +173,7 @@ process referenceGenome_index{
     tag "Downloading"
 
     publishDir "${params.outdir}/reference_genome", mode: 'copy'
-    
+
     input:
     val x from refgen_index_trigger
     file refgen from refgen_referenceGenome_index.mix(refgen_referenceGenome_index_down)
@@ -182,7 +182,7 @@ process referenceGenome_index{
     file "index" into refgen_index_down
 
     when: params.integrate || !(params.arriba || params.ericscript || params.fusioncatcher || params.genefuse || params.integrate)
-    
+
     shell:
     '''
     #!/bin/bash
@@ -191,11 +191,11 @@ process referenceGenome_index{
 
     mkdir index && cd "$_"
     cp ../!{refgen} .
-    
+
     bwa index hg38.fa
 
     '''
-    
+
 }
 
 /*
@@ -211,7 +211,7 @@ process referenceGenome_index{
 process ericsctipt_downloader{
     tag "Downloading"
 
-    publishDir "${params.outdir}/ericscript/files", mode: 'copy'
+    storeDir "${params.outdir}/ericscript/files"
 
     input:
     val x from ch1_ericscript
@@ -220,7 +220,7 @@ process ericsctipt_downloader{
     file "ericscript_db_homosapiens_ensembl84" into ch3_ericscript
 
     when: params.ericscript || !(params.arriba || params.ericscript || params.fusioncatcher || params.genefuse || params.integrate)
-    
+
     script:
     """
     #!/bin/bash
@@ -229,7 +229,7 @@ process ericsctipt_downloader{
 
     curl -O -J -L https://osf.io/54s6h/download
     tar -xf ericscript_db_homosapiens_ensembl84.tar.bz2
-    
+
     rm ericscript_db_homosapiens_ensembl84.tar.bz2
     """
 
@@ -240,7 +240,7 @@ process ericsctipt_downloader{
 process ericscript{
     tag "${pair_id}"
 
-    publishDir "${params.outdir}/ericscript", mode: 'copy'
+    publishDir "${params.outdir}/ericscript", mode: 'move'
 
     input:
     tuple pair_id, file(rna_reads), file(ericscript_db) from rna_reads_ericscript.combine(ch2_ericscript.mix(ch3_ericscript))
@@ -249,16 +249,16 @@ process ericscript{
     file "output/${pair_id}" optional true into ericscript_fusions
 
     when: params.ericscript || !(params.arriba || params.ericscript || params.fusioncatcher || params.genefuse || params.integrate)
-    
+
     script:
     reads = "../${rna_reads[0]} ../${rna_reads[1]}" //reads = params.single_end ? rna_reads[0] : "../${rna_reads[0]} ../${rna_reads[1]}"
     """
     #!/bin/bash
-    
-    export PATH="${params.envPath_ericscript}:$PATH" 
+
+    export PATH="${params.envPath_ericscript}:$PATH"
 
     mkdir output && cd output
-    
+
     ericscript.pl -o ./${pair_id} -db ../${ericscript_db} ${reads}
     """
 
@@ -271,7 +271,7 @@ process ericscript{
 process arriba_downloader{
     tag "Downloading"
 
-    publishDir "${params.outdir}/arriba", mode: 'copy'
+    storeDir "${params.outdir}/arriba"
 
     input:
     val x from ch1_arriba
@@ -280,15 +280,15 @@ process arriba_downloader{
     file "files" into ch3_arriba
 
     when: params.arriba || !(params.arriba || params.ericscript || params.fusioncatcher || params.genefuse || params.integrate)
-    
+
     shell:
     '''
     #!/bin/bash
 
     export PATH="!{params.envPath_arriba}bin:$PATH"
-    
+
     mkdir files && cd "$_"
-   
+
     !{params.envPath_arriba}var/lib/arriba/download_references.sh GRCh38+ENSEMBL93
     '''
 
@@ -297,7 +297,7 @@ process arriba_downloader{
 process arriba{
     tag "${pair_id}"
 
-    publishDir "${params.outdir}/arriba", mode: 'copy'
+    publishDir "${params.outdir}/arriba", mode: 'move'
 
     input:
     tuple pair_id, file(rna_reads), file(arriba_ref) from rna_reads_arriba.combine(ch2_arriba.mix(ch3_arriba))
@@ -310,11 +310,11 @@ process arriba{
     script:
     """
     #!/bin/bash
-    
-    export PATH="${params.envPath_arriba}bin:$PATH" 
+
+    export PATH="${params.envPath_arriba}bin:$PATH"
 
     run_arriba.sh ${arriba_ref}/STAR_index_GRCh38_ENSEMBL93/ ${arriba_ref}/ENSEMBL93.gtf ${arriba_ref}/GRCh38.fa ${params.envPath_arriba}var/lib/arriba/blacklist_hg19_hs37d5_GRCh37_v2.1.0.tsv.gz ${params.envPath_arriba}var/lib/arriba/known_fusions_hg19_hs37d5_GRCh37_v2.1.0.tsv.gz ${params.envPath_arriba}var/lib/arriba/protein_domains_hg19_hs37d5_GRCh37_v2.1.0.gff3 ${params.nthreads} ${rna_reads}
-    
+
     mkdir output && mkdir output/${pair_id}
     mv *.out output/${pair_id}
     mv *.tsv output/${pair_id}
@@ -331,7 +331,7 @@ process arriba{
 process fusioncatcher_downloader{
     tag "Downloading"
 
-    publishDir "${params.outdir}/fusioncatcher", mode: 'copy'
+    storeDir "${params.outdir}/fusioncatcher"
 
     input:
     val x from ch1_fusioncatcher
@@ -340,7 +340,7 @@ process fusioncatcher_downloader{
     file "files" into ch3_fusioncatcher
 
     when: params.fusioncatcher || !(params.arriba || params.ericscript || params.fusioncatcher || params.genefuse || params.integrate)
-    
+
     shell:
     '''
     #!/bin/bash
@@ -351,9 +351,9 @@ process fusioncatcher_downloader{
     wget http://sourceforge.net/projects/fusioncatcher/files/data/human_v102.tar.gz.ab
     wget http://sourceforge.net/projects/fusioncatcher/files/data/human_v102.tar.gz.ac
     wget http://sourceforge.net/projects/fusioncatcher/files/data/human_v102.tar.gz.ad
-    
+
     cat human_v102.tar.gz.* | tar xz
-    ln -s human_v102 current 
+    ln -s human_v102 current
     '''
 
 }
@@ -361,7 +361,7 @@ process fusioncatcher_downloader{
 process fusioncatcher{
     tag "${pair_id}"
 
-    publishDir "${params.outdir}/fusioncatcher", mode: 'copy'
+    publishDir "${params.outdir}/fusioncatcher", mode: 'move'
 
     input:
     tuple pair_id, file(rna_reads), file(fusioncatcher_db) from rna_reads_fusioncatcher.combine(ch2_fusioncatcher.mix(ch3_fusioncatcher))
@@ -376,8 +376,8 @@ process fusioncatcher{
     """
     #!/bin/bash
 
-    export PATH="${params.envPath_fusioncatcher}:$PATH" 
-    
+    export PATH="${params.envPath_fusioncatcher}:$PATH"
+
     fusioncatcher -d ${fusioncatcher_db}/human_v102 -i ${reads} -o output/${pair_id}
     """
 
@@ -390,7 +390,7 @@ process fusioncatcher{
 process integrate_downloader{
     tag "Downloading"
 
-    publishDir "${params.outdir}/integrate", mode: 'copy'
+    storeDir "${params.outdir}/integrate"
 
     input:
     val x from ch1_integrate
@@ -399,14 +399,14 @@ process integrate_downloader{
     file "files" into ch5_integrate, ch6_integrate, ch7_integrate
 
     when: params.integrate || !(params.arriba || params.ericscript || params.fusioncatcher || params.genefuse || params.integrate)
-    
+
     shell:
     '''
     #!/bin/bash
 
     export PATH="!{params.envPath_integrate}:$PATH"
 
-    mkdir files && cd "$_" 
+    mkdir files && cd "$_"
 
     wget https://genome-idx.s3.amazonaws.com/bt/GRCh38_noalt_as.zip
     unzip GRCh38_noalt_as.zip
@@ -417,10 +417,10 @@ process integrate_downloader{
     curl -O -J -L https://osf.io/gv7sq/download
     tar -xvf INTEGRATE.0.2.6.tar.gz
     rm INTEGRATE.0.2.6.tar.gz
-    
-    cd INTEGRATE_0_2_6 && mkdir INTEGRATE-build && cd "$_" 
-    cmake ../Integrate/ -DCMAKE_BUILD_TYPE=release 
-    make 
+
+    cd INTEGRATE_0_2_6 && mkdir INTEGRATE-build && cd "$_"
+    cmake ../Integrate/ -DCMAKE_BUILD_TYPE=release
+    make
     '''
 
 }
@@ -442,12 +442,12 @@ process integrate_builder{
     file "bwts" into ch8_integrate
 
     when: params.integrate || !(params.arriba || params.ericscript || params.fusioncatcher || params.genefuse || params.integrate)
-    
+
     shell:
     '''
     #!/bin/bash
 
-    export PATH="!{params.envPath_integrate}:$PATH" 
+    export PATH="!{params.envPath_integrate}:$PATH"
 
     LD_LIBRARY_PATH=/usr/local/lib
     LD_LIBRARY_PATH=$LD_LIBRARY_PATH:!{integrate_db}/INTEGRATE_0_2_6/INTEGRATE-build/vendor/src/libdivsufsort-2.0.1-build/lib/
@@ -476,7 +476,7 @@ process integrate_converter{
     """
     #!/bin/bash
 
-    export PATH="${params.envPath_integrate}:$PATH" 
+    export PATH="${params.envPath_integrate}:$PATH"
 
     tophat --no-coverage-search ${integrate_db}/GRCh38_noalt_as/GRCh38_noalt_as ${rna_reads}
 
@@ -509,7 +509,7 @@ process integrate_converter{
 process integrate{
     tag "${pair_id}"
 
-    publishDir "${params.outdir}/integrate", mode: 'copy'
+    publishDir "${params.outdir}/integrate", mode: 'move'
 
     input:
     tuple pair_id, file(input), file(integrate_db), file(refgen), file(bwts) from integrate_input.combine(ch3_integrate.mix(ch6_integrate)).combine(refgen_integrate.mix(refgen_integrate_down)).combine(ch2_integrate_bwts.mix(ch8_integrate))
@@ -523,10 +523,10 @@ process integrate{
     '''
     #!/bin/bash
 
-    export PATH="!{params.envPath_integrate}:$PATH" 
+    export PATH="!{params.envPath_integrate}:$PATH"
 
     cp !{input}/* .
-  
+
     parallel samtools index ::: *.bam
 
     LD_LIBRARY_PATH=/usr/local/lib
@@ -549,7 +549,7 @@ process integrate{
 process genefuse_downloader{
     tag "Downloading"
 
-    publishDir "${params.outdir}/genefuse", mode: 'copy'
+    storeDir "${params.outdir}/genefuse"
 
     input:
     val x from ch1_genefuse
@@ -558,7 +558,7 @@ process genefuse_downloader{
     file "files" into ch3_genefuse
 
     when: params.genefuse || !(params.arriba || params.ericscript || params.fusioncatcher || params.genefuse || params.integrate)
-    
+
     shell:
     '''
     #!/bin/bash
@@ -583,7 +583,7 @@ process genefuse_converter{
 
     input:
     tuple pair_id, file(wgstinput) from dna_reads_tumor_genefuse
-    
+
     output:
     tuple pair_id, file("input/${pair_id}") into genefuse_input
 
@@ -593,8 +593,8 @@ process genefuse_converter{
     """
     #!/bin/bash
 
-    export PATH="${params.envPath_genefuse}:$PATH" 
-    
+    export PATH="${params.envPath_genefuse}:$PATH"
+
     mkdir input && mkdir input/${pair_id}
 
     if ${params.dnabam} && ${integrateWGSt}; then
@@ -611,7 +611,7 @@ process genefuse_converter{
 process genefuse{
     tag "${pair_id}"
 
-    publishDir "${params.outdir}/genefuse", mode: 'copy'
+    publishDir "${params.outdir}/genefuse", mode: 'move'
 
     input:
     tuple pair_id, file(input), file(refgen), file(genefuse_db) from genefuse_input.combine(refgen_genefuse.mix(refgen_genefuse_down)).combine(ch2_genefuse.mix(ch3_genefuse))
@@ -625,7 +625,7 @@ process genefuse{
     """
     #!/bin/bash
 
-    export PATH="${params.envPath_genefuse}:$PATH" 
+    export PATH="${params.envPath_genefuse}:$PATH"
 
     cp ${input}/* .
 

From cb81f1c2e729abad2e1a0841f4dbf2a21ae4e1f2 Mon Sep 17 00:00:00 2001
From: Gianpaolo <bitrix@hotmail.it>
Date: Fri, 14 Jan 2022 17:25:57 +0100
Subject: [PATCH 2/7] skip downloader removed

---
 pipeline.nf | 42 ++++++++++++++++--------------------------
 1 file changed, 16 insertions(+), 26 deletions(-)

diff --git a/pipeline.nf b/pipeline.nf
index 7e41ffb..10b0766 100644
--- a/pipeline.nf
+++ b/pipeline.nf
@@ -1,3 +1,14 @@
+
+/******************************************************************************
+ *                                                                            *
+ * Copyright (C) 2022 Politecnico di Torino       *
+ * All Rights Reserved.                                                       *
+ *                                                                            *
+ ******************************************************************************/
+/**
+ * @file pipeline.nf
+ * @authors: Federica Citarella, Bontempo Gianpaolo, Marta Lovino
+ */
 #!/usr/bin/env nextflow
 
 def helpMessage() {
@@ -55,27 +66,6 @@ if (params.help) {
     exit 0
 }
 
-// Files and folders set up from default directories or directories defined in command line
-refDir_refgen = file(params.referenceGenome)
-refDir_refgen_index = file(params.referenceGenome_index)
-
-refFile_ericscript = file(params.ericscript_ref)
-refDir_arriba = file(params.arriba_ref)
-refDir_fusioncatcher = file(params.fusioncatcher_ref)
-refDir_integrate = file(params.integrate_ref)
-refDir_integrate_bwts = file(params.integrate_bwts)
-refDir_genefuse = file(params.genefuse_ref)
-
-// Skip variables set up to verify the existence of files and folders and eventually skip the download processes execution
-params.skip_refgen = refDir_refgen.exists()
-params.skip_refgen_index = refDir_refgen_index.exists()
-
-params.skip_ericscript = refFile_ericscript.exists()
-params.skip_arriba = refDir_arriba.exists()
-params.skip_fusioncatcher= refDir_fusioncatcher.exists()
-params.skip_integrate = refDir_integrate.exists()
-params.skip_integrate_bulder = refDir_integrate_bwts.exists()
-params.skip_genefuse = refDir_genefuse.exists()
 
 // INTEGRATE variables set up (this variable could be modified, for this reason they cannot be defined in the configuration file)
 integrateWGSt = false
@@ -127,13 +117,13 @@ Channel.fromPath(params.integrate_bwts).set{ input_ch1_bwts }
 Channel.fromPath(params.genefuse_ref).set{ input_ch1_genefuse }
 
 (refgen_downloader , refgen_integrate , refgen_integrate_builder, refgen_integrate_converter, refgen_genefuse, refgen_referenceGenome_index) = ( params.skip_refgen ? [Channel.empty(), input_ch1_refgen, input_ch2_refgen, input_ch3_refgen, input_ch4_refgen, input_ch5_refgen] : [input_ch1_refgen, Channel.empty(), Channel.empty(), Channel.empty(), Channel.empty(), Channel.empty()] )
-(refgen_index_trigger , refgen_index) = ( (params.skip_refgen_index || params.dnabam) ? [Channel.empty(), input_ch1_refgen_index] : [input_ch1_refgen_index, Channel.empty()] )
+(refgen_index_trigger , refgen_index) = (params.dnabam ? [Channel.empty(), input_ch1_refgen_index] : [input_ch1_refgen_index, Channel.empty()] )
 
 (ch1_ericscript, ch2_ericscript) =  [input_ch_ericscript, Channel.empty()]
-(ch1_arriba, ch2_arriba) = ( params.skip_arriba ? [Channel.empty(), input_ch_arriba] : [input_ch_arriba, Channel.empty()] )
-(ch1_fusioncatcher , ch2_fusioncatcher) = ( params.skip_fusioncatcher ? [Channel.empty(), input_ch_fusioncatcher] : [input_ch_fusioncatcher, Channel.empty()] )
-(ch1_integrate , ch2_integrate , ch3_integrate, ch4_integrate) = ( params.skip_integrate ? [Channel.empty(), input_ch1_integrate, input_ch2_integrate, input_ch3_integrate] : [input_ch1_integrate, Channel.empty(), Channel.empty(), Channel.empty()] )
-(ch1_integrate_bwts , ch2_integrate_bwts) = ( params.skip_integrate_bulder ? [Channel.empty(), input_ch1_bwts] : [input_ch1_bwts, Channel.empty()] )
+(ch1_arriba, ch2_arriba) =  [input_ch_arriba, Channel.empty()]
+(ch1_fusioncatcher , ch2_fusioncatcher) = [input_ch_fusioncatcher, Channel.empty()]
+(ch1_integrate , ch2_integrate , ch3_integrate, ch4_integrate) = [input_ch1_integrate, Channel.empty(), Channel.empty(), Channel.empty()]
+(ch1_integrate_bwts , ch2_integrate_bwts) = [input_ch1_bwts, Channel.empty()]
 (ch1_genefuse , ch2_genefuse ) = [input_ch1_genefuse, Channel.empty()]
 
 /*

From 73ac7ba6ed4bed0e6967304c850b9b2152a8528f Mon Sep 17 00:00:00 2001
From: Gianpaolo <bitrix@hotmail.it>
Date: Fri, 14 Jan 2022 17:46:18 +0100
Subject: [PATCH 3/7] readme renamed

---
 README.txt => README.md | 18 ++++++++++++------
 1 file changed, 12 insertions(+), 6 deletions(-)
 rename README.txt => README.md (87%)

diff --git a/README.txt b/README.md
similarity index 87%
rename from README.txt
rename to README.md
index 4b380ca..662ad12 100644
--- a/README.txt
+++ b/README.md
@@ -1,25 +1,31 @@
-QUICK START:
+# GeneFusion: a nextflow-based application
 
 1. Install Nextflow and Docker.
-     
+
 2. Test the pipeline:
-        
+
         nextflow run federicacitarrella/FusionFlow -profile [test_docker/test_local]
 
 4. Run your own analysis:
-        
+
         nextflow run federicacitarrella/FusionFlow \
-                --rnareads “/path/to/rna/reads_{1,2}.*” \ 
+                --rnareads “/path/to/rna/reads_{1,2}.*” \
                 --dnareads_tumor “/path/to/dna/tumor/reads_{3,4}.*” \
                 --dnareads_normal “/path/to/dna/normal/reads_{5,6}.*” \
                 --arriba --ericscript --fusioncatcher --integrate --genefuse \
                 -profile <docker/local>
 
 Before using the local profile you need to create conda virtual environments from the yml files and specify the environment path in the command line (the Arriba path does not need "/bin").
+
+
+
 e.g. nextflow run federicacitarrella/FusionFlow \
         --envPath_ericscript /path/to/miniconda3/envs/ericscript/bin \
         --envPath_arriba /path/to/miniconda3/envs/arriba/ \
         --envPath_fusioncatcher /path/to/miniconda3/envs/fusioncatcher/bin \
         --envPath_integrate /path/to/miniconda3/envs/integrate/bin \
         --envPath_genefuse /path/to/miniconda3/envs/genefuse/bin \
-         -profile test_local
\ No newline at end of file
+         -profile test_local
+
+
+# Acknowledgments
\ No newline at end of file

From 9e1780fd636189ad0bed1ea1d6ea5168e6e95662 Mon Sep 17 00:00:00 2001
From: Gianpaolo <bitrix@hotmail.it>
Date: Wed, 19 Jan 2022 09:52:43 +0000
Subject: [PATCH 4/7] config changed

---
 nextflow.config | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

diff --git a/nextflow.config b/nextflow.config
index b3cb8a9..292d1b1 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -2,7 +2,7 @@ manifest {
     mainScript = 'pipeline.nf'
 }
 
-params { 
+params {
   help = false
   dnabam = false
   single_end = false
@@ -36,33 +36,34 @@ params {
   envPath_genefuse = "/opt/conda/envs/genefuse/bin"
 
   nthreads = 8
-  max_cpus = 16  
-} 
+  max_cpus = 16
+}
 
 process {
     container = 'federicacitarrella/pipeline:latest'
     publishDir = [path: params.outdir, mode: 'copy', overwrite: 'true']
-} 
+    memory= '10GB'
+}
 
 profiles {
     local {
-      params.feelnc_opts = "--monoex=1 --size=50 --minfrac_over=1.0 " 
+      params.feelnc_opts = "--monoex=1 --size=50 --minfrac_over=1.0 "
     }
     docker {
-      params.feelnc_opts = "--monoex=1 --size=50 --minfrac_over=1.0 " 
+      params.feelnc_opts = "--monoex=1 --size=50 --minfrac_over=1.0 "
       docker.enabled = true
       docker.fixOwnership = true
     }
     test_docker{
       params.rnareads  = "$baseDir/tutorial/reads_{1,2}.fq.gz"
       params.dnareads_tumor  = "$baseDir/tutorial/reads_{3,4}.fq.gz"
-      params.feelnc_opts = "--monoex=1 --size=50 --minfrac_over=1.0 " 
+      params.feelnc_opts = "--monoex=1 --size=50 --minfrac_over=1.0 "
       docker.enabled = true
       docker.fixOwnership = true
     }
     test_local{
       params.rnareads  = "$baseDir/tutorial/reads_{1,2}.fq.gz"
       params.dnareads_tumor  = "$baseDir/tutorial/reads_{3,4}.fq.gz"
-      params.feelnc_opts = "--monoex=1 --size=50 --minfrac_over=1.0 " 
+      params.feelnc_opts = "--monoex=1 --size=50 --minfrac_over=1.0 "
     }
 }
\ No newline at end of file

From 3b7d8a31fc2a8139965a4fccd4437bd6ba8b75dd Mon Sep 17 00:00:00 2001
From: Gianpaolo <bitrix@hotmail.it>
Date: Wed, 19 Jan 2022 10:17:32 +0000
Subject: [PATCH 5/7] config changed

---
 nextflow.config | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index 292d1b1..79b1e52 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -42,7 +42,11 @@ params {
 process {
     container = 'federicacitarrella/pipeline:latest'
     publishDir = [path: params.outdir, mode: 'copy', overwrite: 'true']
-    memory= '10GB'
+}
+
+executor {
+    name   = 'local'
+    memory = '9GB'
 }
 
 profiles {

From 68c7baa85561856d64eec7831207769de34720db Mon Sep 17 00:00:00 2001
From: Gianpaolo <bitrix@hotmail.it>
Date: Thu, 20 Jan 2022 02:53:49 +0000
Subject: [PATCH 6/7] small fixies

---
 pipeline.nf | 10 +++-------
 1 file changed, 3 insertions(+), 7 deletions(-)

diff --git a/pipeline.nf b/pipeline.nf
index 7e41ffb..0991dfd 100644
--- a/pipeline.nf
+++ b/pipeline.nf
@@ -147,9 +147,6 @@ process referenceGenome_downloader{
     // publishDir publishes the output in a specific folder with copy mode
     storeDir "${params.outdir}/reference_genome"
 
-    input:
-    val trigger from refgen_downloader
-
     output:
     file "hg38.fa" into refgen_integrate_builder_down, refgen_integrate_converter_down, refgen_referenceGenome_index_down, refgen_integrate_down, refgen_genefuse_down
 
@@ -213,8 +210,6 @@ process ericsctipt_downloader{
 
     storeDir "${params.outdir}/ericscript/files"
 
-    input:
-    val x from ch1_ericscript
 
     output:
     file "ericscript_db_homosapiens_ensembl84" into ch3_ericscript
@@ -240,18 +235,19 @@ process ericsctipt_downloader{
 process ericscript{
     tag "${pair_id}"
 
-    publishDir "${params.outdir}/ericscript", mode: 'move'
+    publishDir "${params.outdir}/ericscript/result", mode: 'move'
 
     input:
     tuple pair_id, file(rna_reads), file(ericscript_db) from rna_reads_ericscript.combine(ch2_ericscript.mix(ch3_ericscript))
 
     output:
-    file "output/${pair_id}" optional true into ericscript_fusions
+    file "output/${pair_id}" into ericscript_fusions
 
     when: params.ericscript || !(params.arriba || params.ericscript || params.fusioncatcher || params.genefuse || params.integrate)
 
     script:
     reads = "../${rna_reads[0]} ../${rna_reads[1]}" //reads = params.single_end ? rna_reads[0] : "../${rna_reads[0]} ../${rna_reads[1]}"
+    println reads
     """
     #!/bin/bash
 

From ddd083340309b352989ef7c05c3dbf8b837017e2 Mon Sep 17 00:00:00 2001
From: gianpaolo <bitrix@hotmail.it>
Date: Thu, 27 Jan 2022 12:25:41 +0100
Subject: [PATCH 7/7] output published correctly

---
 nextflow.config | 19 +++++++++++--------
 pipeline.nf     |  9 ++++-----
 2 files changed, 15 insertions(+), 13 deletions(-)

diff --git a/nextflow.config b/nextflow.config
index 79b1e52..ee06846 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -29,24 +29,27 @@ params {
   dnareads_tumor = ""
   dnareads_normal = ""
 
-  envPath_ericscript = "/opt/conda/envs/ericscript/bin"
-  envPath_arriba = "/opt/conda/envs/arriba/"
-  envPath_fusioncatcher = "/opt/conda/envs/fusioncatcher/bin"
-  envPath_integrate = "/opt/conda/envs/integrate/bin"
-  envPath_genefuse = "/opt/conda/envs/genefuse/bin"
+  envPath_ericscript = "/homes/gbontempo/.conda/envs/ericscript/bin"
+  envPath_arriba = "/homes/gbontempo/.conda/envs/arriba/"
+  envPath_fusioncatcher = "/homes/gbontempo/.conda/envs/fusioncatcher/bin"
+  envPath_integrate = "/homes/gbontempo/.conda/envs/integrate/bin"
+  envPath_genefuse = "/homes/gbontempo/.conda/envs/genefuse/bin"
 
   nthreads = 8
   max_cpus = 16
 }
 
 process {
+    executor = "slurm"
+    memory = '20GB'
+    queue= 'prod'
+    cpus= 3
     container = 'federicacitarrella/pipeline:latest'
-    publishDir = [path: params.outdir, mode: 'copy', overwrite: 'true']
 }
 
 executor {
-    name   = 'local'
-    memory = '9GB'
+    memory = '20GB'
+
 }
 
 profiles {
diff --git a/pipeline.nf b/pipeline.nf
index 0991dfd..c924f1a 100644
--- a/pipeline.nf
+++ b/pipeline.nf
@@ -241,8 +241,7 @@ process ericscript{
     tuple pair_id, file(rna_reads), file(ericscript_db) from rna_reads_ericscript.combine(ch2_ericscript.mix(ch3_ericscript))
 
     output:
-    file "output/${pair_id}" into ericscript_fusions
-
+    file "output/${pair_id}/*" into ericscript_fusions
     when: params.ericscript || !(params.arriba || params.ericscript || params.fusioncatcher || params.genefuse || params.integrate)
 
     script:
@@ -273,7 +272,7 @@ process arriba_downloader{
     val x from ch1_arriba
 
     output:
-    file "files" into ch3_arriba
+    file "files/**" into ch3_arriba
 
     when: params.arriba || !(params.arriba || params.ericscript || params.fusioncatcher || params.genefuse || params.integrate)
 
@@ -333,7 +332,7 @@ process fusioncatcher_downloader{
     val x from ch1_fusioncatcher
 
     output:
-    file "files" into ch3_fusioncatcher
+    file "files/*" into ch3_fusioncatcher
 
     when: params.fusioncatcher || !(params.arriba || params.ericscript || params.fusioncatcher || params.genefuse || params.integrate)
 
@@ -363,7 +362,7 @@ process fusioncatcher{
     tuple pair_id, file(rna_reads), file(fusioncatcher_db) from rna_reads_fusioncatcher.combine(ch2_fusioncatcher.mix(ch3_fusioncatcher))
 
     output:
-    file "output/${pair_id}" optional true into fusioncatcher_fusions
+    file "output/${pair_id}/*" optional true into fusioncatcher_fusions
 
     when: params.fusioncatcher || !(params.arriba || params.ericscript || params.fusioncatcher || params.genefuse || params.integrate)