Update config.yml

IARCbioinfo · May 23, 2019 · a9c91c9 · a9c91c9
1 parent 5eacbe1
commit a9c91c9
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -13,8 +13,8 @@ jobs:
         - run: cd ~/project/NGS_data_test/1000G_CEU_TP53/ && nextflow run ~/project/needlestack.nf -with-docker iarcbioinfo/needlestack --bed TP53_exon2_11.bed --nsplit 4 --ref 17.fasta.gz --input_bams BAM/ --output_vcf all_variants.vcf  && cp all_variants.vcf results/$CIRCLE_BRANCH/test2.vcf && mkdir -p results/$CIRCLE_BRANCH/PDF/test2 && cp PDF/*.pdf results/$CIRCLE_BRANCH/PDF/test2/ && sudo rm -rf work/ .nextflow.* trace.txt* timeline.html* all_variants.vcf PDF/
         - run: cd ~/project/NGS_data_test/1000G_CEU_TP53/ && nextflow run ~/project/needlestack.nf -with-docker iarcbioinfo/needlestack --bed TP53_exon2_11.bed --nsplit 1 --ref 17.fasta.gz --input_bams BAM/ --output_vcf all_variants.vcf  && cp all_variants.vcf results/$CIRCLE_BRANCH/test3.vcf && mkdir -p results/$CIRCLE_BRANCH/PDF/test3 && cp PDF/*.pdf results/$CIRCLE_BRANCH/PDF/test3/ && sudo rm -rf work/ .nextflow.* trace.txt* timeline.html* all_variants.vcf PDF/
         - run: cd ~/project/NGS_data_test/1000G_CEU_TP53/ && nextflow run ~/project/needlestack.nf -with-docker iarcbioinfo/needlestack --region 17:7572816-7572816 --ref 17.fasta.gz --input_bams BAM/ --output_vcf all_variants.vcf --min_ao 0 --all_SNVs && cp all_variants.vcf results/$CIRCLE_BRANCH/test4.vcf && mkdir -p results/$CIRCLE_BRANCH/PDF/test4 && cp PDF/*.pdf results/$CIRCLE_BRANCH/PDF/test4/ && sudo rm -rf work/ .nextflow.* trace.txt* timeline.html* all_variants.vcf PDF/
-        - run: cd ~/project/NGS_data_test/1000G_CEU_TP53/ && nextflow run ~/project/needlestack.nf -with-docker iarcbioinfo/needlestack --region 17:7578176-7578288 --nsplit 4 --ref 17.fasta.gz --input_bams BAM/ --output_vcf all_variants.vcf --no_plots --use_file_name --no_indels && cp all_variants.vcf results/$CIRCLE_BRANCH/test5.vcf && mkdir -p results/$CIRCLE_BRANCH/PDF/test5 && sudo rm -rf work/ .nextflow.* trace.txt* timeline.html* all_variants.vcf
-        - run: cd ~/project/NGS_data_test/1000G_CEU_TP53/ && nextflow run ~/project/needlestack.nf -with-docker iarcbioinfo/needlestack --region 17:7580000-7580004--nsplit 4 --ref 17.fasta.gz --input_bams BAM/ --output_vcf all_variants.vcf && cp all_variants.vcf results/$CIRCLE_BRANCH/test6.vcf && mkdir -p results/$CIRCLE_BRANCH/PDF/test6 && sudo rm -rf work/ .nextflow.* trace.txt* timeline.html* all_variants.vcf
+        - run: cd ~/project/NGS_data_test/1000G_CEU_TP53/ && nextflow run ~/project/needlestack.nf -with-docker iarcbioinfo/needlestack --region 17:7578176-7578288 --nsplit 4 --ref 17.fasta.gz --input_bams BAM/ --output_vcf all_variants.vcf --no_plots --use_file_name --no_indels && cp all_variants.vcf results/$CIRCLE_BRANCH/test5.vcf && mkdir -p results/$CIRCLE_BRANCH/PDF/test5 && sudo rm -rf work/ .nextflow.* trace.txt* timeline.html* all_variants.vcf PDF/
+        - run: cd ~/project/NGS_data_test/1000G_CEU_TP53/ && nextflow run ~/project/needlestack.nf -with-docker iarcbioinfo/needlestack --region 17:7580000-7580004--nsplit 4 --ref 17.fasta.gz --input_bams BAM/ --output_vcf all_variants.vcf && cp all_variants.vcf results/$CIRCLE_BRANCH/test6.vcf && mkdir -p results/$CIRCLE_BRANCH/PDF/test6 && sudo rm -rf work/ .nextflow.* trace.txt* timeline.html* all_variants.vcf PDF/
         - deploy:
             branch: [dev, master]
             command: chmod +x deploy.sh && ./deploy.sh