fixing commiting too many files

.github/PULL_REQUEST_TEMPLATE.md

@@ -16,6 +16,8 @@
 
 - [ ] Input and output files are being symlinked into the `CFG["inputs"]` and `CFG["outputs"]` subdirectories, respectively.
 
+- [ ] I grouped the input symlinking rule to the next job that uses the input files. 
+
 - [ ] I updated the final target rule (`*_all`) to include every output rule.
 
 - [ ] I explained important module design decisions in `CHANGELOG.md`.
@@ -48,4 +50,11 @@
 
 ## Checklist for Updated Module
 
-To be completed.
+Important! If you are updating the module version, ensure the previous version of the module is restored from master.
+If you want to restore a deleted file or directory from the remote master, you can use `git checkout origin/master path/to/file`,
+then a `git commit` will ensure that file is tracked on your branch again.
+Example:
+```
+mv modules/strelka/1.1 modules/strelka/1.2
+git checkout origin/master modules/strelka/1.1
+```

demo/data/samples.tsv

@@ -2,3 +2,5 @@ sample_id	seq_type	patient_id	tissue_status	genome_build	strand	read_length
 TCRBOA7-N-WEX	capture	TCRBOA7	normal	grch37	positive	100
 TCRBOA7-T-WEX	capture	TCRBOA7	tumour	grch37	positive	100
 TCRBOA7-T-RNA	mrna	TCRBOA7	tumour	grch37	positive	100
+TCRBOA7-N-WGS	genome	TCRBOA7	normal	grch37	positive	100
+TCRBOA7-T-WGS	genome	TCRBOA7	tumour	grch37	positive	100

demo/dry-run.sh

@@ -1,6 +1,18 @@
 #!/bin/bash
 
+# Launches a snakefile of your choice in dry run mode (for debugging)
+# Usage: ./dry_run.sh <snakefile.smk> <target_rule> "<snakemake_flags>"
+# Example: ./dry_run.sh example.smk example_all 
+# snakefile.smk The snakefile you want to run
+# target_rule: The name of one of the target rules specified in one of the included Snakefiles
+# snakemake_flags: One or more flags for the snakemake to run, specified inside quotation marks
+
+
 # Default to all targets
-TARGETS=${@:-all}
+snakefile=$1
+TARGETS=${2:-all}
+snakemake_flags=$3
+
+snakemake --dryrun --cores 24 $snakemake_flags -s $snakefile --printshellcmds --reason --use-conda $TARGETS
+
 
-snakemake --dryrun --cores 24 --printshellcmds --reason --use-conda $TARGETS

demo/run.sh

@@ -1,7 +1,18 @@
 #!/bin/bash
 
+
+# Launches a snakefile of your choice in dry run mode (for debugging)
+# Usage: ./dry_run.sh <snakefile.smk> <target_rule> "<snakemake_flags>"
+# Example: ./dry_run.sh example.smk example_all
+# snakefile.smk The snakefile you want to run
+# target_rule: The name of one of the target rules specified in one of the included Snakefiles
+# snakemake_flags: One or more flags for the snakemake to run, specified inside quotation marks
+
+
 # Default to all targets
-TARGETS=${@:-all}
+snakefile=$1
+TARGETS=${2:-all}
+snakemake_flags=$3
 
 # Determine the number of available cores for parallelization
 NUM_CORES=$(grep -c '^processor' /proc/cpuinfo)
@@ -17,4 +28,6 @@ if (( $CORES_AVAILABLE <= 0 )); then
     echo "Check out top/htop to see what other jobs are currently running."
     exit 1
 fi
-nice -n 10 snakemake --cores "${CORES_AVAILABLE}" --keep-going --latency-wait 120 --use-conda "$TARGETS"
+nice -n 10 snakemake --cores "${CORES_AVAILABLE}" $snakemake_flags -s $snakefile --keep-going --latency-wait 120 --use-conda $TARGETS
+
+

docs/source/for_developers.rst

@@ -21,7 +21,7 @@ Getting Started
       # conda create -n lcr-modules "python>=3.6"
       # conda activate lcr-modules
       
-      conda install cookiecutter git
+      conda install -c conda-forge cookiecutter
 
 4. Clone the `lcr-modules repository`_ and the `lcr-scripts repository`_.