Merge branch 'main' into hotfix-gui-targ

CCBR · Aug 16, 2024 · 0e06b20 · 0e06b20
2 parents dd7509e + 315ef23
commit 0e06b20
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diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml
@@ -23,71 +23,63 @@ jobs:
         run: |
           docker run -v $PWD:/opt2 snakemake/snakemake:v7.32.4 \
           /opt2/bin/xavier run --input \
-          /opt2/.tests/Sample10_ARK1_S37.R1.fastq.gz /opt2/.tests/Sample10_ARK1_S37.R2.fastq.gz \
-          /opt2/.tests/Sample11_ACI_158_S38.R1.fastq.gz /opt2/.tests/Sample11_ACI_158_S38.R2.fastq.gz \
-          /opt2/.tests/Sample4_CRL1622_S31.R1.fastq.gz /opt2/.tests/Sample4_CRL1622_S31.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/Sample10_ARK1_S37.R1.fastq.gz /opt2/.tests/Sample10_ARK1_S37.R2.fastq.gz \
-          /opt2/.tests/Sample11_ACI_158_S38.R1.fastq.gz /opt2/.tests/Sample11_ACI_158_S38.R2.fastq.gz \
-          /opt2/.tests/Sample4_CRL1622_S31.R1.fastq.gz /opt2/.tests/Sample4_CRL1622_S31.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/Sample10_ARK1_S37.R1.fastq.gz /opt2/.tests/Sample10_ARK1_S37.R2.fastq.gz \
-          /opt2/.tests/Sample11_ACI_158_S38.R1.fastq.gz /opt2/.tests/Sample11_ACI_158_S38.R2.fastq.gz \
-          /opt2/.tests/Sample4_CRL1622_S31.R1.fastq.gz /opt2/.tests/Sample4_CRL1622_S31.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/Sample10_ARK1_S37.R1.fastq.gz /opt2/.tests/Sample10_ARK1_S37.R2.fastq.gz \
-          /opt2/.tests/Sample11_ACI_158_S38.R1.fastq.gz /opt2/.tests/Sample11_ACI_158_S38.R2.fastq.gz \
-          /opt2/.tests/Sample4_CRL1622_S31.R1.fastq.gz /opt2/.tests/Sample4_CRL1622_S31.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
 
       - name: Tumor-normal BAM Dry Run
         run: |
           docker run -v $PWD:/opt2 snakemake/snakemake:v7.32.4 \
           /opt2/bin/xavier run --input \
-          /opt2/.tests/Sample10_ARK1_S37.recal.bam \
-          /opt2/.tests/Sample11_ACI_158_S38.recal.bam \
-          /opt2/.tests/Sample4_CRL1622_S31.recal.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/Sample10_ARK1_S37.recal.bam \
-          /opt2/.tests/Sample11_ACI_158_S38.recal.bam \
-          /opt2/.tests/Sample4_CRL1622_S31.recal.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/Sample10_ARK1_S37.recal.bam \
-          /opt2/.tests/Sample11_ACI_158_S38.recal.bam \
-          /opt2/.tests/Sample4_CRL1622_S31.recal.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/Sample10_ARK1_S37.recal.bam \
-          /opt2/.tests/Sample11_ACI_158_S38.recal.bam \
-          /opt2/.tests/Sample4_CRL1622_S31.recal.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/README.md
diff --git a/.tests/Sample10_ARK1_S37.R1.fastq.gz b/.tests/Sample10_ARK1_S37.R1.fastq.gz
diff --git a/.tests/Sample10_ARK1_S37.R2.fastq.gz b/.tests/Sample10_ARK1_S37.R2.fastq.gz
diff --git a/.tests/Sample10_ARK1_S37.recal.bam b/.tests/Sample10_ARK1_S37.recal.bam
diff --git a/.tests/Sample11_ACI_158_S38.R1.fastq.gz b/.tests/Sample11_ACI_158_S38.R1.fastq.gz
diff --git a/.tests/Sample11_ACI_158_S38.R2.fastq.gz b/.tests/Sample11_ACI_158_S38.R2.fastq.gz
diff --git a/.tests/Sample11_ACI_158_S38.recal.bam b/.tests/Sample11_ACI_158_S38.recal.bam
diff --git a/.tests/Sample4_CRL1622_S31.R1.fastq.gz b/.tests/Sample4_CRL1622_S31.R1.fastq.gz
diff --git a/.tests/Sample4_CRL1622_S31.R2.fastq.gz b/.tests/Sample4_CRL1622_S31.R2.fastq.gz
diff --git a/.tests/Sample4_CRL1622_S31.recal.bam b/.tests/Sample4_CRL1622_S31.recal.bam
diff --git a/.tests/pairs.tsv b/.tests/pairs.tsv
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -8,6 +8,7 @@
 - Provide default exome targets for hg38 and mm10, which can be overridden by the optional `--targets` argument. (#102, @kelly-sovacool)
   - Previously, the `--targets` argument was required with no defaults.
 - Increased memory for rules: BWA mem, qualimap, kraken. gatk_contamination is not localrule. (#89, @samarth8392)
+- Added new human test dataset for github workflow (#27, @samarth8392)
 - fixes minor bug in GUI related to choosing the correct default target file (#108, @samarth8392)
 
 ## XAVIER 3.0.3

diff --git a/docs/usage/run.md b/docs/usage/run.md
@@ -46,7 +46,9 @@ Each of the following arguments are required. Failure to provide a required argu
 >
 > One or more FastQ files can be provided. The pipeline does NOT support single-end WES data. Please provide either a set of FastQ files or a set of BAM files. The pipeline does NOT support processing a mixture of FastQ files and BAM files. From the command-line, each input file should separated by a space. Globbing is supported! This makes selecting FastQ files easy. Input FastQ files should be gzipp-ed.
 >
-> **_Example:_** `--input .tests/*.R?.fastq.gz`
+> **_Example:_** `--input tests/data/*.R?.fastq.gz`
+>
+> **_Example:_** `--input /data/CCBR_Pipeliner/testdata/XAVIER/human_subset/*.R?.fastq.gz`
 
 ---
 
@@ -251,15 +253,15 @@ module purge
 module load ccbrpipeliner
 
 # Step 2A.) Initialize the all resources to the output folder
-xavier run --input .tests/*.R?.fastq.gz \
+xavier run --input tests/data/*.R?.fastq.gz \
                  --output /data/$USER/xavier_hg38 \
                  --genome hg38 \
                  --targets Agilent_SSv7_allExons_hg38.bed \
                  --mode slurm \
                  --runmode init
 
 # Step 2B.) Dry-run the pipeline
-xavier run --input .tests/*.R?.fastq.gz \
+xavier run --input tests/data/*.R?.fastq.gz \
                  --output /data/$USER/xavier_hg38 \
                  --genome hg38 \
                  --targets Agilent_SSv7_allExons_hg38.bed \
@@ -269,11 +271,18 @@ xavier run --input .tests/*.R?.fastq.gz \
 # Step 2C.) Run the XAVIER pipeline
 # The slurm mode will submit jobs to the cluster.
 # It is recommended running xavier in this mode.
-xavier run --input .tests/*.R?.fastq.gz \
+xavier run --input tests/data/*.R?.fastq.gz \
                  --output /data/$USER/xavier_hg38 \
                  --genome hg38 \
                  --targets Agilent_SSv7_allExons_hg38.bed \
                  --mode slurm \
                  --runmode run
 
 ```
+
+The example dataset in `tests/data` in this repository is a very small
+subsampled dataset, and some steps of the pipeline fail due to the small size
+(CNV callling, somalier, etc).
+We have a larger subsample (25% of a full human dataset) available on Biowulf if
+you would like to test the full functionality of the pipeline:
+`/data/CCBR_Pipeliner/testdata/XAVIER/human_subset/*.R?.fastq.gz`
diff --git a/pyproject.toml b/pyproject.toml
@@ -64,7 +64,7 @@ Repository = "https://github.com/CCBR/XAVIER"
 xavier = "."
 
 [tool.setuptools.package-data]
-"*" = ["CITATION.cff", "LICENSE", "VERSION", "docker/**", "resources/**", "bin/**", "config/**", "resources/**", "workflow/**", "tests/**", ".tests/**"]
+"*" = ["CITATION.cff", "LICENSE", "VERSION", "docker/**", "resources/**", "bin/**", "config/**", "resources/**", "workflow/**", "tests/**"]
 
 [tool.setuptools.dynamic]
 version = {file = "VERSION"}

diff --git a/src/xavier/__main__.py b/src/xavier/__main__.py
@@ -220,7 +220,7 @@ def parsed_arguments():
                                 FastQ files or a set of BAM files. The pipeline does
                                 NOT support processing a mixture of FastQ files and
                                 BAM files.
-                                Example: --input .tests/*.R?.fastq.gz
+                                Example: --input tests/data/*.R?.fastq.gz
           --output OUTPUT
                                 Path to an output directory. This location is where
                                 the pipeline will create all of its output files, also
@@ -256,15 +256,15 @@ def parsed_arguments():
           # Step 2A.) Initialize the pipeline
           xavier run \\
                         --runmode init \\
-                        --input .tests/*.R?.fastq.gz \\
+                        --input tests/data/*.R?.fastq.gz \\
                         --output /data/$USER/xavier_hg38 \\
                         --genome hg38 \\
                         --targets resources/Agilent_SSv7_allExons_hg38.bed
 
           # Step 2B.) Dry-run the pipeline
           xavier run \\
                         --runmode dryrun \\
-                        --input .tests/*.R?.fastq.gz \\
+                        --input tests/data/*.R?.fastq.gz \\
                         --output /data/$USER/xavier_hg38 \\
                         --genome hg38 \\
                         --targets resources/Agilent_SSv7_allExons_hg38.bed \\
@@ -275,7 +275,7 @@ def parsed_arguments():
           # It is recommended running xavier in this mode.
           xavier run \\
                         --runmode run \\
-                        --input .tests/*.R?.fastq.gz \\
+                        --input tests/data/*.R?.fastq.gz \\
                         --output /data/$USER/xavier_hg38 \\
                         --genome hg38 \\
                         --targets resources/Agilent_SSv7_allExons_hg38.bed \\

diff --git a/tests/data/README.md b/tests/data/README.md
@@ -0,0 +1,20 @@
+# About
+
+These input files are used for continuous integration purposes, specifically to dry run the pipeline whenever commits have been made to the main, master, or unified branches.
+
+Human whole exome sequence reads from the Sequencing Quality Control Phase 2 (SEQC2) Consortium has been subsampled and added. 
+
+The tumor-normal paired reads were downloaded from the [seqc2](https://sites.google.com/view/seqc2/home/sequencing) server that were sequenced by the NCI (WES_NC_T_1 vs. WES_NC_N_1) which corresponds to NCBI SRA accession no. [SRX4728524](https://www.ncbi.nlm.nih.gov/sra/SRX4728524) and [SRX4728523](https://www.ncbi.nlm.nih.gov/sra/SRX4728523) respectively. 
+
+Next, the reads were subsampled to 0.1% using `seqtk` and gzipped as follows:
+
+```bash
+seqtk sample -s100 {input}.R[1/2].fastq.gz 0.001 > {input}.R[1/2]_sub.R2.fastq
+gzip *.fastq
+```
+
+Similarly, the BAM files were created by first mapping to the hg38 genome and then subsampled using `samtools`:
+
+```bash
+samtools view -s 0.00125 -b WES_NC_[T/N]_1.bam -o WES_NC_[T/N]_1_sub.bam
+```
diff --git a/tests/data/WES_NC_N_1_sub.R1.fastq.gz b/tests/data/WES_NC_N_1_sub.R1.fastq.gz
diff --git a/tests/data/WES_NC_N_1_sub.R2.fastq.gz b/tests/data/WES_NC_N_1_sub.R2.fastq.gz
diff --git a/tests/data/WES_NC_N_1_sub.bam b/tests/data/WES_NC_N_1_sub.bam
diff --git a/tests/data/WES_NC_T_1_sub.R1.fastq.gz b/tests/data/WES_NC_T_1_sub.R1.fastq.gz
diff --git a/tests/data/WES_NC_T_1_sub.R2.fastq.gz b/tests/data/WES_NC_T_1_sub.R2.fastq.gz
diff --git a/tests/data/WES_NC_T_1_sub.bam b/tests/data/WES_NC_T_1_sub.bam
diff --git a/tests/data/pairs.tsv b/tests/data/pairs.tsv
@@ -0,0 +1,2 @@
+Normal	Tumor
+WES_NC_N_1_sub	WES_NC_T_1_sub
diff --git a/tests/test_cli.py b/tests/test_cli.py
@@ -8,8 +8,8 @@
 
 xavier_run = (
     "xavier run "
-    "--input .tests/*.fastq.gz "
-    "--pairs .tests/pairs.tsv "
+    "--input tests/data/*.fastq.gz "
+    "--pairs tests/data/pairs.tsv "
     "--mode local "
 )
 

diff --git a/tests/test_run.py b/tests/test_run.py
@@ -15,14 +15,14 @@ def test_dryrun():
         with tempfile.TemporaryDirectory() as tmp_dir:
             run_args = argparse.Namespace(
                 runmode="init",
-                input=list(glob.glob(f"{xavier_base('.tests')}/*.fastq.gz")),
+                input=list(glob.glob(f"{xavier_base('tests/data')}/*.fastq.gz")),
                 output=tmp_dir,
                 genome="hg38",
                 targets=xavier_base("resources/Agilent_SSv7_allExons_hg38.bed"),
                 mode="local",
                 job_name="pl:xavier",
                 callers=["mutect2", "mutect", "strelka", "vardict", "varscan"],
-                pairs=xavier_base(".tests/pairs.tsv"),
+                pairs=xavier_base("tests/data/pairs.tsv"),
                 ffpe=False,
                 cnv=False,
                 wait=False,