From 6720d88f4e46e67b9a225f06bfb10c8e8ae04a84 Mon Sep 17 00:00:00 2001
From: WackerO <43847497+WackerO@users.noreply.github.com>
Date: Fri, 15 Jul 2022 11:20:58 +0200
Subject: [PATCH] Fgbio tmpdir modification (#1890)

* Updated container versions for fgbio groupreadsbyumi and callmolecularconsensusreads

* Corrected fgbio call container, trying to fix fgbio group tests

* Removed incorrect line

* Changed tmp-dir to .

* Update modules/fgbio/groupreadsbyumi/main.nf

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>

* Update modules/fgbio/fastqtobam/main.nf

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>

* Added callmol and sortbam

* fixed typo in callmol container

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
---
 modules/fgbio/callmolecularconsensusreads/main.nf | 1 +
 modules/fgbio/fastqtobam/main.nf                  | 3 +--
 modules/fgbio/groupreadsbyumi/main.nf             | 3 +--
 modules/fgbio/sortbam/main.nf                     | 7 ++++---
 4 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/modules/fgbio/callmolecularconsensusreads/main.nf b/modules/fgbio/callmolecularconsensusreads/main.nf
index fc9b1b1b..88c5ab4c 100644
--- a/modules/fgbio/callmolecularconsensusreads/main.nf
+++ b/modules/fgbio/callmolecularconsensusreads/main.nf
@@ -22,6 +22,7 @@ process FGBIO_CALLMOLECULARCONSENSUSREADS {
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     fgbio \\
+        --tmp-dir=. \\
         CallMolecularConsensusReads \\
         -i $bam \\
         $args \\
diff --git a/modules/fgbio/fastqtobam/main.nf b/modules/fgbio/fastqtobam/main.nf
index 51b6b72c..76cfc075 100644
--- a/modules/fgbio/fastqtobam/main.nf
+++ b/modules/fgbio/fastqtobam/main.nf
@@ -22,10 +22,9 @@ process FGBIO_FASTQTOBAM {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    mkdir tmp
 
     fgbio \\
-        --tmp-dir=${PWD}/tmp \\
+        --tmp-dir=. \\
         FastqToBam \\
         -i $reads \\
         -o "${prefix}_umi_converted.bam" \\
diff --git a/modules/fgbio/groupreadsbyumi/main.nf b/modules/fgbio/groupreadsbyumi/main.nf
index 7c09ab7c..3014355c 100644
--- a/modules/fgbio/groupreadsbyumi/main.nf
+++ b/modules/fgbio/groupreadsbyumi/main.nf
@@ -24,10 +24,9 @@ process FGBIO_GROUPREADSBYUMI {
     def prefix = task.ext.prefix ?: "${meta.id}"
 
     """
-    mkdir tmp
 
     fgbio \\
-        --tmp-dir=${PWD}/tmp \\
+        --tmp-dir=. \\
         GroupReadsByUmi \\
         -s $strategy \\
         $args \\
diff --git a/modules/fgbio/sortbam/main.nf b/modules/fgbio/sortbam/main.nf
index 5026987c..bb718d0b 100644
--- a/modules/fgbio/sortbam/main.nf
+++ b/modules/fgbio/sortbam/main.nf
@@ -2,10 +2,10 @@ process FGBIO_SORTBAM {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::fgbio=1.3.0" : null)
+    conda (params.enable_conda ? "bioconda::fgbio=2.0.2" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/fgbio:1.3.0--0' :
-        'quay.io/biocontainers/fgbio:1.3.0--0' }"
+        'https://depot.galaxyproject.org/singularity/fgbio:2.0.2--hdfd78af_0' :
+        'quay.io/biocontainers/fgbio:2.0.2--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)
@@ -22,6 +22,7 @@ process FGBIO_SORTBAM {
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     fgbio \\
+        --tmp-dir=. \\
         SortBam \\
         -i $bam \\
         $args \\