fixed TMPDIR to use current working directory across all processes

Author: maurya-anand

modules/local/adapter_trim/main.nf

@@ -16,7 +16,7 @@ process ADAPTER_TRIM {
     def fq2_base = fastq_2.toString().tokenize('.')[0]
     """
     set -euo pipefail
-    export TMPDIR=${task.workDir}
+    export TMPDIR=\$PWD
     total_threads=${task.cpus}
     trim_galore \
         --paired \

modules/local/alignment/main.nf

@@ -13,7 +13,7 @@ process STAR_ALIGNMENT_WASP {
     script:
     """
     set -euo pipefail
-    export TMPDIR=${task.workDir}
+    export TMPDIR=\$PWD
     STAR \\
     --runMode alignReads \\
     --runThreadN ${task.cpus} \\
@@ -25,7 +25,7 @@ process STAR_ALIGNMENT_WASP {
     --readFilesCommand zcat \\
     --outSAMtype BAM SortedByCoordinate \\
     --outSAMunmapped Within \\
-    --outTmpDir ${task.workDir}/_STARtmp \\
+    --outTmpDir \$PWD/_STARtmp \\
     --outFileNamePrefix ${meta.sampleid}. \\
     --outFilterMultimapNmax 20 \\
     --alignSJoverhangMin 8 \\

modules/local/allele_count/main.nf

@@ -13,7 +13,7 @@ process ALLELE_COUNT{
     """
     set -euo pipefail
     
-    export TMPDIR=${task.workDir}
+    export TMPDIR=\$PWD
 
     [[ -f "${reference_fa}.fai" ]] || samtools faidx ${reference_fa}
 

modules/local/index_genome/main.nf

@@ -9,7 +9,7 @@ process STAR_GENOME_INDEX {
     script:
     """
     set -euo pipefail
-    export TMPDIR=${task.workDir}
+    export TMPDIR=\$PWD
 
     mkdir -p STAR_INDEX
 
@@ -18,6 +18,6 @@ process STAR_GENOME_INDEX {
       --genomeDir STAR_INDEX \\
       --genomeFastaFiles ${ref_fa} \\
       --sjdbGTFfile ${gtf} \\
-      --outTmpDir ${task.workDir}/_STARgenomeTmp
+      --outTmpDir \$PWD/_STARgenomeTmp
     """
 }

modules/local/report/main.nf

@@ -10,7 +10,7 @@ process REPORT {
 
     script:
     """
-    export TMPDIR=${task.workDir}
+    export TMPDIR=\$PWD
     multiqc --no-ai .
     """
 }

modules/local/subset_1kgp/main.nf

@@ -9,7 +9,7 @@ process SUBSET_1KGP_VCF {
 
     script:
     """
-    export TMPDIR=${task.workDir}
+    export TMPDIR=\$PWD
 
     total_threads=${task.cpus}
 
@@ -56,7 +56,7 @@ process SUBSET_1KGP_VCF {
         } > list.txt
 
         bcftools concat --threads \${total_threads} -f list.txt -Ou \\
-            | bcftools sort --temp-dir ${task.workDir} -Ov -o ${meta.sampleid}.1KGP.snps.het.vcf
+            | bcftools sort --temp-dir \$PWD -Ov -o ${meta.sampleid}.1KGP.snps.het.vcf
     else
         echo "Phased VCF dir is empty. Creating empty output files."
         touch ${meta.sampleid}.1KGP.snps.het.vcf