Merge pull request #82 from IARCbioinfo/dev

Updated circleCI test after storeDir to publishDir (#80)

circle.yml

@@ -18,29 +18,29 @@ test:
       nextflow run ~/needlestack/needlestack.nf -with-docker iarcbioinfo/needlestack --bed TP53_all.bed --nsplit 4 --fasta_ref 17.fasta.gz --bam_folder BAM/ --min_dp 50 
       cp BAM/all_variants.vcf results/$CIRCLE_BRANCH/test1.vcf 
       mkdir -p results/$CIRCLE_BRANCH/PDF/test1
-      cp BAM/VCF/*.pdf results/$CIRCLE_BRANCH/PDF/test1/
-      rm -rf work/ .nextflow.* BAM/all_variants.vcf BAM/VCF/ BAM/PILEUP/ BAM/BED_REGIONS/ 
+      cp BAM/PDF/*.pdf results/$CIRCLE_BRANCH/PDF/test1/
+      rm -rf work/ .nextflow.* BAM/all_variants.vcf BAM/PDF/ 
     - |
       cd ~/NGS_data_test/1000G_CEU_TP53/
       nextflow run ~/needlestack/needlestack.nf -with-docker iarcbioinfo/needlestack --bed TP53_exon2_11.bed --nsplit 4 --fasta_ref 17.fasta.gz --bam_folder BAM/ --min_dp 50 
       cp BAM/all_variants.vcf results/$CIRCLE_BRANCH/test2.vcf 
       mkdir -p results/$CIRCLE_BRANCH/PDF/test2
-      cp BAM/VCF/*.pdf results/$CIRCLE_BRANCH/PDF/test2/
-      rm -rf work/ .nextflow.* BAM/all_variants.vcf BAM/VCF/ BAM/PILEUP/ BAM/BED_REGIONS/ 
+      cp BAM/PDF/*.pdf results/$CIRCLE_BRANCH/PDF/test2/
+      rm -rf work/ .nextflow.* BAM/all_variants.vcf BAM/PDF/ 
     - |
       cd ~/NGS_data_test/1000G_CEU_TP53/
       nextflow run ~/needlestack/needlestack.nf -with-docker iarcbioinfo/needlestack:stable --bed TP53_all.bed --nsplit 4 --fasta_ref 17.fasta.gz --bam_folder BAM/ --min_dp 50 
       cp BAM/all_variants.vcf results/$CIRCLE_BRANCH/test1_stable.vcf 
       mkdir -p results/$CIRCLE_BRANCH/PDF/test1_stable
-      cp BAM/VCF/*.pdf results/$CIRCLE_BRANCH/PDF/test1_stable/
-      rm -rf work/ .nextflow.* BAM/all_variants.vcf BAM/VCF/ BAM/PILEUP/ BAM/BED_REGIONS/ 
+      cp BAM/PDF/*.pdf results/$CIRCLE_BRANCH/PDF/test1_stable/
+      rm -rf work/ .nextflow.* BAM/all_variants.vcf BAM/PDF/ 
     - |
       cd ~/NGS_data_test/1000G_CEU_TP53/
       nextflow run ~/needlestack/needlestack.nf -with-docker iarcbioinfo/needlestack:stable --bed TP53_exon2_11.bed --nsplit 4 --fasta_ref 17.fasta.gz --bam_folder BAM/ --min_dp 50 
       cp BAM/all_variants.vcf results/$CIRCLE_BRANCH/test2_stable.vcf 
       mkdir -p results/$CIRCLE_BRANCH/PDF/test2_stable
-      cp BAM/VCF/*.pdf results/$CIRCLE_BRANCH/PDF/test2_stable/
-      rm -rf work/ .nextflow.* BAM/all_variants.vcf BAM/VCF/ BAM/PILEUP/ BAM/BED_REGIONS/ 
+      cp BAM/PDF/*.pdf results/$CIRCLE_BRANCH/PDF/test2_stable/
+      rm -rf work/ .nextflow.* BAM/all_variants.vcf BAM/PDF/ 
 deployment:
   git:
     branch: [master, dev]