Merge pull request #224 from hoelzer-lab/fix_webgestalt_missing_organism

Fix webgestalt missing organism
hoelzer-lab · Aug 15, 2023 · 094be4d · 094be4d
2 parents 7767b87 + 95360fc
commit 094be4d
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Showing 7 changed files with 16 additions and 2 deletions.
diff --git a/configs/conda.config b/configs/conda.config
@@ -3,6 +3,7 @@ process {
     withLabel:	minimap2	{ conda = "$baseDir/envs/minimap2.yaml" } 
     withLabel:	python3	{ conda = "$baseDir/envs/python3.yaml" } 
     withLabel:	deseq2	{ conda = "$baseDir/envs/deseq2.yaml" } 
+    withLabel:	webgestalt	{ conda = "$baseDir/envs/webgestalt.yaml" } 
     withLabel:	fastp	{ conda = "$baseDir/envs/fastp.yaml" } 
     withLabel:	fastqc	{ conda = "$baseDir/envs/fastqc.yaml" } 
     withLabel:	nanoplot	{ conda = "$baseDir/envs/nanoplot.yaml" } 

diff --git a/configs/container.config b/configs/container.config
@@ -3,6 +3,7 @@ process {
     withLabel:	minimap2	{ container = "nanozoo/minimap2:2.22--b178b67" } 
     withLabel:	python3	{ container = "nanozoo/python_rnaseq:3--23823db" } 
     withLabel:	deseq2	{ container = "nanozoo/deseq2:1.34.0--c670fa0" } 
+    withLabel:	webgestalt	{ container = "nanozoo/webgestalt:0.4.6--5a8d95e" } 
     withLabel:	fastp	{ container = "nanozoo/fastp:0.23.1--9f2e255" } 
     withLabel:	fastqc	{ container = "nanozoo/fastqc:0.11.8--fbfa1d7" } 
     withLabel:	subread	{ container = "nanozoo/subread:2.0.1--713a8e7" } 

diff --git a/configs/local.config b/configs/local.config
@@ -2,6 +2,7 @@ process {
     withLabel: hisat2 { cpus = params.cores } 
     withLabel: minimap2 { cpus = params.cores } 
     withLabel: deseq2 { cpus = params.cores } 
+    withLabel: webgestalt { cpus = params.cores } 
     withLabel: fastp { cpus = params.cores } 
     withLabel: fastqc { cpus = 1 } 
     withLabel: subread { cpus = params.cores } 

diff --git a/configs/nodes.config b/configs/nodes.config
@@ -11,4 +11,5 @@ process {
     withLabel: dammit { cpus = 42 ; memory = '42 GB' }
     withLabel: rattle { cpus = 32; memory = '32 GB' }
     withLabel: smallTask { cpus = 1; memory = '1 GB' }
+    withLabel: webgestalt { cpus = 1; memory = '4 GB' }
 }
diff --git a/envs/deseq2.yaml b/envs/deseq2.yaml
@@ -22,7 +22,6 @@ dependencies:
   - r-openxlsx=4.2.5
   - r-doparallel=1.0.17
   - r-foreach=1.5.2
-  - r-webgestaltr=0.4.4
   - r-upsetr=1.4.0
   - r-sessioninfo=1.2.2
   - r-knitcitations=1.0.12

diff --git a/envs/webgestalt.yaml b/envs/webgestalt.yaml
@@ -0,0 +1,9 @@
+name: webgestalt
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - r-base
+  - r-webgestaltr=0.4.6
+  - zip==3.0
diff --git a/modules/webgestalt.nf b/modules/webgestalt.nf
@@ -1,5 +1,5 @@
 process webgestalt {
-    label 'deseq2'
+    label 'webgestalt'
     tag "$comparison"
 
     publishDir "${params.output}/${params.deseq2_dir}/${comparison}/downstream_analysis", mode: 'copy', pattern: "WebGestalt"
@@ -19,6 +19,8 @@ process webgestalt {
     script:
     comparison = resFold05.toString().split("deseq2_")[1].split("_filtered")[0]//findAll("[a-zA-Z]*_vs_[a-zA-Z]*")[0]
     """
+    # set env var for zip command for zipping in webgestalt since sometimes its not set in conda envs somehow and crashes the report making
+    export R_ZIPCMD=\$(which zip)
     R CMD BATCH --no-save --no-restore '--args c(".") c("${resFold05}") c("${species}") c("${id_type}")' ${webgestalt_script}
     """
 }