[MODIF] update tpm folder #24

CHANGELOG.md

@@ -5,15 +5,16 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## v1.3.0dev
 
+* Change the /tmp/ folder by ./tmp/ folder so that all tmp files are now in the work (#24)
 * Add `--hicpro_maps` options to generate the raw and normalized HiC-Pro maps. The default is now to use cooler
-* Add HiCExplorer distance decay quality control
-* Add HiCExplorer TADs calling
-* Add insulation score TADs calling
-* Generate cooler/h5/txt contact maps
+* Add HiCExplorer distance decay quality control (#54)
+* Add HiCExplorer TADs calling (#55)
+* Add insulation score TADs calling (#55)
+* Generate cooler/txt contact maps
 * Normalize Hi-C data with cooler instead of iced
 * New `--digestion` parameter to automatically set the restriction_site and ligation_site motifs
 * New `--keep_multi` and `keep_dup` options. Default: false
-* Template update for nf-core/tools v1.11
+* Template update for nf-core/tools
 * Minor fix to summary log messages in pipeline header
 
 ### `Fixed`

main.nf

@@ -514,7 +514,7 @@ if (!params.dnase){
                      ${bam1} ${bam2}
 
       samtools sort -@ ${task.cpus} -m 800M \\
-      	            -n -T /tmp/ \\
+      	            -n -T ./tmp/ \\
 	            -o ${prefix}_bwt2merged.sorted.bam \\
 	            ${prefix}_bwt2merged.bam
 
@@ -635,7 +635,7 @@ if (!params.dnase){
       prefix = pe_bam.toString() - ~/.bam/
       """
       mapped_2hic_fragments.py -f ${frag_file} -r ${pe_bam} --all ${opts}
-      sort -T /tmp/ -k2,2V -k3,3n -k5,5V -k6,6n -o ${prefix}.validPairs ${prefix}.validPairs
+      sort -T ./tmp/ -k2,2V -k3,3n -k5,5V -k6,6n -o ${prefix}.validPairs ${prefix}.validPairs
       """
    }
 }
@@ -663,7 +663,7 @@ else{
       prefix = pe_bam.toString() - ~/.bam/
       """
       mapped_2hic_dnase.py -r ${pe_bam} ${opts}
-      sort -T /tmp/ -k2,2V -k3,3n -k5,5V -k6,6n -o ${prefix}.validPairs ${prefix}.validPairs
+      sort -T ./tmp/ -k2,2V -k3,3n -k5,5V -k6,6n -o ${prefix}.validPairs ${prefix}.validPairs
       """
    }
 }
@@ -690,7 +690,7 @@ process remove_duplicates {
    mkdir -p stats/${sample}
 
    ## Sort valid pairs and remove read pairs with same starts (i.e duplicated read pairs)
-   sort -T /tmp/ -S 50% -k2,2V -k3,3n -k5,5V -k6,6n -m ${vpairs} | \
+   sort -T ./tmp/ -S 50% -k2,2V -k3,3n -k5,5V -k6,6n -m ${vpairs} | \
    awk -F"\\t" 'BEGIN{c1=0;c2=0;s1=0;s2=0}(c1!=\$2 || c2!=\$5 || s1!=\$3 || s2!=\$6){print;c1=\$2;c2=\$5;s1=\$3;s2=\$6}' > ${sample}.allValidPairs
 
    echo -n "valid_interaction\t" > stats/${sample}/${sample}_allValidPairs.mergestat