Merge pull request #130 from CCBR/latency-wait

fix: increase file latency wait
CCBR · Nov 19, 2024 · d2d6269 · d2d6269
2 parents a2f8618 + b95e4c8
commit d2d6269
Show file tree

Hide file tree

Showing 9 changed files with 9 additions and 191 deletions.
diff --git a/.github/workflows/activeDev_linter.yaml b/.github/workflows/activeDev_linter.yaml
diff --git a/.github/workflows/main_linter.yaml b/.github/workflows/main_linter.yaml
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -9,6 +9,7 @@
   - Also use `python -E` to ensure the `$PYTHONPATH` is not carried over. (#129, @kelly-sovacool)
 - Fix `reconfig` to correctly replace variables in the config file. (#121, @kelly-sovacool)
 - Prevent using excessive memory when copying reference files. (#126, @kelly-sovacool)
+- Fix missing output files due to file system latency and use real (absolute) paths where possible. (#130, @kelly-sovacool)
 
 ## CHARLIE 0.11.0
 

diff --git a/charlie b/charlie
@@ -481,7 +481,7 @@ function run() {
     --use-singularity \
     --singularity-args "$SINGULARITY_BINDS" \
     --use-envmodules \
-    --latency-wait 120 \
+    --latency-wait 300 \
     --configfile $CONFIGFILE \
     --cores all \
     --rerun-incomplete \
@@ -521,7 +521,7 @@ snakemake -s $SNAKEFILE \
     --singularity-args "$SINGULARITY_BINDS" \
     --use-envmodules \
     --printshellcmds \
-    --latency-wait 120 \
+    --latency-wait 300 \
     --configfile $CONFIGFILE \
     --cluster-config $CLUSTERFILE \
     --cluster "$CLUSTER_SBATCH_CMD" \
@@ -562,7 +562,7 @@ EOF
     --use-singularity \
     --singularity-args "$SINGULARITY_BINDS" \
     --printshellcmds \
-    --latency-wait 120 \
+    --latency-wait 300 \
     --configfile $CONFIGFILE \
     --cluster-config $CLUSTERFILE \
     --cluster "$CLUSTER_SBATCH_CMD" \
@@ -640,6 +640,7 @@ function main(){
   esac
   done
 
+  WORKDIR=$(readlink -f $WORKDIR)
   echo "Working Dir: $WORKDIR"
 
   if [[ -z "$SING_CACHE_DIR" ]]; then

diff --git a/config/biowulf/config.yaml b/config/biowulf/config.yaml
@@ -107,7 +107,7 @@ high_confidence_core_callers_plus_n: 1
 
 ciri_perl_script: "/opt2/CIRI_v2.0.6/CIRI2.pl" # path in docker container
 # change this path to a directory containing fasta and GTF files for all host and virus genomes
-fastas_gtfs_dir: "/data/CCBR_Pipeliner/db/PipeDB/charlie/fastas_gtfs"
+fastas_gtfs_dir: "/gpfs/gsfs10/users/CCBR_Pipeliner/db/PipeDB/charlie/fastas_gtfs"
 
 annotation_lookups:
   hg38: "PIPELINE_HOME/resources/hg38_2_hg19_lookup.txt"

diff --git a/config/lint.config.yaml b/config/lint.config.yaml
diff --git a/config/samples.tsv b/config/samples.tsv
@@ -1,3 +1,3 @@
 sampleName	path_to_R1_fastq	path_to_R2_fastq
-GI1_N	/data/CCBR_Pipeliner/testdata/circRNA/human/GI1_N_ss.R1.fastq.gz	/data/CCBR_Pipeliner/testdata/circRNA/human/GI1_N_ss.R2.fastq.gz
-GI1_T	/data/CCBR_Pipeliner/testdata/circRNA/human/GI1_T_ss.R1.fastq.gz
+GI1_N	/gpfs/gsfs10/users/CCBR_Pipeliner/testdata/circRNA/human/GI1_N_ss.R1.fastq.gz	/gpfs/gsfs10/users/CCBR_Pipeliner/testdata/circRNA/human/GI1_N_ss.R2.fastq.gz
+GI1_T	/gpfs/gsfs10/users/CCBR_Pipeliner/testdata/circRNA/human/GI1_T_ss.R1.fastq.gz
diff --git a/lintit b/lintit
diff --git a/workflow/rules/findcircrna.smk b/workflow/rules/findcircrna.smk
@@ -1104,6 +1104,7 @@ postProcessStarAlignment.pl \\
     --starDir ${{starDir}}/ \\
     --outDir ${{outDir}}/
 
+sleep 10
 echo -ne "chr\\tstart\\tend\\tstrand\\tread_count\\n" > {output.ctf}
 awk -F"\\t" -v OFS="\\t" -v minreads={params.bsj_min_nreads} '{{if ($5>=minreads) {{print $1,$2,$3,$6,$5}}}}' {output.bed} >> {output.ctf}