change requirements according to Patrick's feedback

TRON-Bioinformatics · Aug 26, 2024 · da57bc5 · da57bc5
1 parent ac1e9a4
commit da57bc5
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Showing 6 changed files with 10 additions and 17 deletions.
diff --git a/.gitignore b/.gitignore
@@ -7,4 +7,9 @@ trace.txt*
 report.html*
 test/output
 conda_env
-__pycache__/
+__pycache__/
+trace*.txt
+dag*.html
+report*.html
+timeline*.html
+venv/
diff --git a/main.nf b/main.nf
@@ -4,7 +4,7 @@ nextflow.enable.dsl = 2
 
 include { FASTP } from './modules/01_qc'
 include { STAR ; STAR_ARRIBA ; READ_FILTER ; BAM2FASTQ } from './modules/02_alignment'
-include { FUSION_CATCHER ; STAR_FUSION ; ARRIBA; FUSION_CATCHER_INDEX } from './modules/03_fusion_callers'
+include { FUSION_CATCHER ; STAR_FUSION ; ARRIBA } from './modules/03_fusion_callers'
 include { FUSION_PARSER ; FUSION_ANNOTATION } from './modules/04_joint_fusion_calling'
 include { FUSION2CSV ; CSV2FASTA ; STAR_INDEX ; FUSION_FILTER ; STAR_CUSTOM ; READ_COUNT } from './modules/05_requantification'
 include { MERGE_DATA ; PREDICTION } from './modules/06_summarize'

diff --git a/modules/01_qc.nf b/modules/01_qc.nf
@@ -1,7 +1,7 @@
 
 process FASTP {
     tag "${name}"
-    label 'process_medium'
+    label 'process_low'
 
     conda ("${baseDir}/environments/qc.yml")
 

diff --git a/modules/02_alignment.nf b/modules/02_alignment.nf
@@ -102,7 +102,7 @@ process READ_FILTER {
 
 process BAM2FASTQ {
     tag "${name}"
-    label 'process_medium'
+    label 'process_low'
 
     conda ("${baseDir}/environments/samtools.yml")
 

diff --git a/modules/03_fusion_callers.nf b/modules/03_fusion_callers.nf
@@ -1,16 +1,4 @@
 
-process FUSION_CATCHER_INDEX {
-    tag "${name}"
-    label 'process_low'
-
-    conda ("${baseDir}/environments/fusioncatcher.yml")
-
-    script:
-    """
-    download-human-db.sh
-    """
-}
-
 
 process FUSION_CATCHER {
     tag "${name}"

diff --git a/modules/05_requantification.nf b/modules/05_requantification.nf
@@ -114,7 +114,7 @@ process STAR_CUSTOM {
 
 process READ_COUNT {
   tag "${name}"
-  label 'process_medium'
+  label 'process_single'
 
   conda ("${baseDir}/environments/requantification.yml")