added temp dir usage

Author: maurya-anand

modules/local/adapter_trim/main.nf

@@ -15,8 +15,9 @@ process ADAPTER_TRIM {
     def fq1_base = fastq_1.toString().tokenize('.')[0]
     def fq2_base = fastq_2.toString().tokenize('.')[0]
     """
-    total_threads=${task.cpus}
     set -euo pipefail
+    export TMPDIR=${task.workDir}
+    total_threads=${task.cpus}
     trim_galore \
         --paired \
         --illumina \

modules/local/alignment/main.nf

@@ -13,7 +13,7 @@ process STAR_ALIGNMENT_WASP {
     script:
     """
     set -euo pipefail
-
+    export TMPDIR=${task.workDir}
     STAR \\
     --runMode alignReads \\
     --runThreadN ${task.cpus} \\
@@ -25,6 +25,7 @@ process STAR_ALIGNMENT_WASP {
     --readFilesCommand zcat \\
     --outSAMtype BAM SortedByCoordinate \\
     --outSAMunmapped Within \\
+    --outTmpDir ${task.workDir} \\
     --outFileNamePrefix ${meta.sampleid}. \\
     --outFilterMultimapNmax 20 \\
     --alignSJoverhangMin 8 \\

modules/local/allele_count/main.nf

@@ -12,6 +12,8 @@ process ALLELE_COUNT{
     script:
     """
     set -euo pipefail
+    
+    export TMPDIR=${task.workDir}
 
     [[ -f "${reference_fa}.fai" ]] || samtools faidx ${reference_fa}
 

modules/local/index_genome/main.nf

@@ -9,13 +9,15 @@ process STAR_GENOME_INDEX {
     script:
     """
     set -euo pipefail
+    export TMPDIR=${task.workDir}
 
     mkdir -p STAR_INDEX
 
     STAR --runMode genomeGenerate \\
       --runThreadN ${task.cpus} \\
       --genomeDir STAR_INDEX \\
       --genomeFastaFiles ${ref_fa} \\
-      --sjdbGTFfile ${gtf}
+      --sjdbGTFfile ${gtf} \\
+      --outTmpDir ${task.workDir}
     """
 }

modules/local/report/main.nf

@@ -10,6 +10,7 @@ process REPORT {
 
     script:
     """
+    export TMPDIR=${task.workDir}
     multiqc --no-ai .
     """
 }

modules/local/subset_1kgp/main.nf

@@ -9,6 +9,8 @@ process SUBSET_1KGP_VCF {
 
     script:
     """
+    export TMPDIR=${task.workDir}
+
     total_threads=${task.cpus}
 
     threads_per_job=\$(( total_threads > 4 ? 4 : total_threads ))
@@ -54,7 +56,7 @@ process SUBSET_1KGP_VCF {
         } > list.txt
 
         bcftools concat -f list.txt -Ou \\
-            | bcftools sort --temp-dir ./ -Ov -o ${meta.sampleid}.1KGP.snps.het.vcf
+            | bcftools sort --temp-dir ${task.workDir} -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