From 6dc37fa1d83ab059065294907c0c6068ac5c250e Mon Sep 17 00:00:00 2001 From: samarth8392 Date: Thu, 15 Aug 2024 14:05:51 -0400 Subject: [PATCH] refactor: change test files location --- .github/workflows/main.yaml | 40 +++++++++--------- {.tests => tests/data}/README.md | 0 .../data}/WES_NC_N_1_sub.R1.fastq.gz | Bin .../data}/WES_NC_N_1_sub.R2.fastq.gz | Bin {.tests => tests/data}/WES_NC_N_1_sub.bam | Bin .../data}/WES_NC_T_1_sub.R1.fastq.gz | Bin .../data}/WES_NC_T_1_sub.R2.fastq.gz | Bin {.tests => tests/data}/WES_NC_T_1_sub.bam | Bin {.tests => tests/data}/pairs.tsv | 0 9 files changed, 20 insertions(+), 20 deletions(-) rename {.tests => tests/data}/README.md (100%) rename {.tests => tests/data}/WES_NC_N_1_sub.R1.fastq.gz (100%) rename {.tests => tests/data}/WES_NC_N_1_sub.R2.fastq.gz (100%) rename {.tests => tests/data}/WES_NC_N_1_sub.bam (100%) rename {.tests => tests/data}/WES_NC_T_1_sub.R1.fastq.gz (100%) rename {.tests => tests/data}/WES_NC_T_1_sub.R2.fastq.gz (100%) rename {.tests => tests/data}/WES_NC_T_1_sub.bam (100%) rename {.tests => tests/data}/pairs.tsv (100%) diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml index 78b3c2a..38dfaca 100644 --- a/.github/workflows/main.yaml +++ b/.github/workflows/main.yaml @@ -23,31 +23,31 @@ jobs: run: | docker run -v $PWD:/opt2 snakemake/snakemake:v7.32.4 \ /opt2/bin/xavier run --input \ - /opt2/.tests/WES_NC_N_1_sub.R1.fastq.gz /opt2/.tests/WES_NC_N_1_sub.R2.fastq.gz \ - /opt2/.tests/WES_NC_T_1_sub.R1.fastq.gz /opt2/.tests/WES_NC_T_1_sub.R2.fastq.gz \ + /opt2/tests/data/WES_NC_N_1_sub.R1.fastq.gz /opt2/tests/data/WES_NC_N_1_sub.R2.fastq.gz \ + /opt2/tests/data/WES_NC_T_1_sub.R1.fastq.gz /opt2/tests/data/WES_NC_T_1_sub.R2.fastq.gz \ --output /opt2/output_tn_fqs --targets /opt2/resources/Agilent_SSv7_allExons_hg38.bed \ - --pairs /opt2/.tests/pairs.tsv --genome hg38 --mode local --ffpe --cnv --runmode init + --pairs /opt2/tests/data/pairs.tsv --genome hg38 --mode local --ffpe --cnv --runmode init docker run -v $PWD:/opt2 snakemake/snakemake:v7.32.4 \ /opt2/bin/xavier run --input \ - /opt2/.tests/WES_NC_N_1_sub.R1.fastq.gz /opt2/.tests/WES_NC_N_1_sub.R2.fastq.gz \ - /opt2/.tests/WES_NC_T_1_sub.R1.fastq.gz /opt2/.tests/WES_NC_T_1_sub.R2.fastq.gz \ + /opt2/tests/data/WES_NC_N_1_sub.R1.fastq.gz /opt2/tests/data/WES_NC_N_1_sub.R2.fastq.gz \ + /opt2/tests/data/WES_NC_T_1_sub.R1.fastq.gz /opt2/tests/data/WES_NC_T_1_sub.R2.fastq.gz \ --output /opt2/output_tn_fqs --targets /opt2/resources/Agilent_SSv7_allExons_hg38.bed \ - --pairs /opt2/.tests/pairs.tsv --genome hg38 --mode local --ffpe --cnv --runmode dryrun + --pairs /opt2/tests/data/pairs.tsv --genome hg38 --mode local --ffpe --cnv --runmode dryrun - name: Tumor-only FastQ Dry Run run: | docker run -v $PWD:/opt2 snakemake/snakemake:v7.32.4 \ /opt2/bin/xavier run --input \ - /opt2/.tests/WES_NC_N_1_sub.R1.fastq.gz /opt2/.tests/WES_NC_N_1_sub.R2.fastq.gz \ - /opt2/.tests/WES_NC_T_1_sub.R1.fastq.gz /opt2/.tests/WES_NC_T_1_sub.R2.fastq.gz \ + /opt2/tests/data/WES_NC_N_1_sub.R1.fastq.gz /opt2/tests/data/WES_NC_N_1_sub.R2.fastq.gz \ + /opt2/tests/data/WES_NC_T_1_sub.R1.fastq.gz /opt2/tests/data/WES_NC_T_1_sub.R2.fastq.gz \ --output /opt2/output_tonly_fqs --targets /opt2/resources/Agilent_SSv7_allExons_hg38.bed \ --genome hg38 --mode local --ffpe --runmode init docker run -v $PWD:/opt2 snakemake/snakemake:v7.32.4 \ /opt2/bin/xavier run --input \ - /opt2/.tests/WES_NC_N_1_sub.R1.fastq.gz /opt2/.tests/WES_NC_N_1_sub.R2.fastq.gz \ - /opt2/.tests/WES_NC_T_1_sub.R1.fastq.gz /opt2/.tests/WES_NC_T_1_sub.R2.fastq.gz \ + /opt2/tests/data/WES_NC_N_1_sub.R1.fastq.gz /opt2/tests/data/WES_NC_N_1_sub.R2.fastq.gz \ + /opt2/tests/data/WES_NC_T_1_sub.R1.fastq.gz /opt2/tests/data/WES_NC_T_1_sub.R2.fastq.gz \ --output /opt2/output_tonly_fqs --targets /opt2/resources/Agilent_SSv7_allExons_hg38.bed \ --genome hg38 --mode local --ffpe --runmode dryrun @@ -55,31 +55,31 @@ jobs: run: | docker run -v $PWD:/opt2 snakemake/snakemake:v7.32.4 \ /opt2/bin/xavier run --input \ - /opt2/.tests/WES_NC_N_1_sub.bam \ - /opt2/.tests/WES_NC_T_1_sub.bam \ + /opt2/tests/data/WES_NC_N_1_sub.bam \ + /opt2/tests/data/WES_NC_T_1_sub.bam \ --output /opt2/output_tn_bams --targets /opt2/resources/Agilent_SSv7_allExons_hg38.bed \ - --pairs /opt2/.tests/pairs.tsv --genome hg38 --mode local --ffpe --cnv --runmode init + --pairs /opt2/tests/data/pairs.tsv --genome hg38 --mode local --ffpe --cnv --runmode init docker run -v $PWD:/opt2 snakemake/snakemake:v7.32.4 \ /opt2/bin/xavier run --input \ - /opt2/.tests/WES_NC_N_1_sub.bam \ - /opt2/.tests/WES_NC_T_1_sub.bam \ + /opt2/tests/data/WES_NC_N_1_sub.bam \ + /opt2/tests/data/WES_NC_T_1_sub.bam \ --output /opt2/output_tn_bams --targets /opt2/resources/Agilent_SSv7_allExons_hg38.bed \ - --pairs /opt2/.tests/pairs.tsv --genome hg38 --mode local --ffpe --cnv --runmode dryrun + --pairs /opt2/tests/data/pairs.tsv --genome hg38 --mode local --ffpe --cnv --runmode dryrun - name: Tumor-only BAM Dry Run run: | docker run -v $PWD:/opt2 snakemake/snakemake:v7.32.4 \ /opt2/bin/xavier run --input \ - /opt2/.tests/WES_NC_N_1_sub.bam \ - /opt2/.tests/WES_NC_T_1_sub.bam \ + /opt2/tests/data/WES_NC_N_1_sub.bam \ + /opt2/tests/data/WES_NC_T_1_sub.bam \ --output /opt2/output_tonly_bams --targets /opt2/resources/Agilent_SSv7_allExons_hg38.bed \ --genome hg38 --mode local --ffpe --runmode init docker run -v $PWD:/opt2 snakemake/snakemake:v7.32.4 \ /opt2/bin/xavier run --input \ - /opt2/.tests/WES_NC_N_1_sub.bam \ - /opt2/.tests/WES_NC_T_1_sub.bam \ + /opt2/tests/data/WES_NC_N_1_sub.bam \ + /opt2/tests/data/WES_NC_T_1_sub.bam \ --output /opt2/output_tonly_bams --targets /opt2/resources/Agilent_SSv7_allExons_hg38.bed \ --genome hg38 --mode local --ffpe --runmode dryrun diff --git a/.tests/README.md b/tests/data/README.md similarity index 100% rename from .tests/README.md rename to tests/data/README.md diff --git a/.tests/WES_NC_N_1_sub.R1.fastq.gz b/tests/data/WES_NC_N_1_sub.R1.fastq.gz similarity index 100% rename from .tests/WES_NC_N_1_sub.R1.fastq.gz rename to tests/data/WES_NC_N_1_sub.R1.fastq.gz diff --git a/.tests/WES_NC_N_1_sub.R2.fastq.gz b/tests/data/WES_NC_N_1_sub.R2.fastq.gz similarity index 100% rename from .tests/WES_NC_N_1_sub.R2.fastq.gz rename to tests/data/WES_NC_N_1_sub.R2.fastq.gz diff --git a/.tests/WES_NC_N_1_sub.bam b/tests/data/WES_NC_N_1_sub.bam similarity index 100% rename from .tests/WES_NC_N_1_sub.bam rename to tests/data/WES_NC_N_1_sub.bam diff --git a/.tests/WES_NC_T_1_sub.R1.fastq.gz b/tests/data/WES_NC_T_1_sub.R1.fastq.gz similarity index 100% rename from .tests/WES_NC_T_1_sub.R1.fastq.gz rename to tests/data/WES_NC_T_1_sub.R1.fastq.gz diff --git a/.tests/WES_NC_T_1_sub.R2.fastq.gz b/tests/data/WES_NC_T_1_sub.R2.fastq.gz similarity index 100% rename from .tests/WES_NC_T_1_sub.R2.fastq.gz rename to tests/data/WES_NC_T_1_sub.R2.fastq.gz diff --git a/.tests/WES_NC_T_1_sub.bam b/tests/data/WES_NC_T_1_sub.bam similarity index 100% rename from .tests/WES_NC_T_1_sub.bam rename to tests/data/WES_NC_T_1_sub.bam diff --git a/.tests/pairs.tsv b/tests/data/pairs.tsv similarity index 100% rename from .tests/pairs.tsv rename to tests/data/pairs.tsv