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Ribodetector and RustQC Additions #47

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Ribodetector and RustQC Additions #47

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a26ddda
Ribodetector and RustQC additions
mikemartinez99 Apr 17, 2026
695b049
Ribodetector params in prebuilt configs
mikemartinez99 Apr 17, 2026
f44fddb
update tests
mikemartinez99 Apr 17, 2026
8e8889f
convert all mem_mb to integers
mikemartinez99 Apr 17, 2026
3ae090d
Fix read_length inclusion in main config
mikemartinez99 Apr 17, 2026
36d47e7
fix gawk error in ribo_stats to work with github action
mikemartinez99 Apr 17, 2026
391c7d8
add gitignore
mikemartinez99 Apr 21, 2026
73344fb
Make RustQC optional
mikemartinez99 Apr 21, 2026
a31ff48
Apply RiboDetector only for paired-end samples
brbergamo Apr 21, 2026
df89afd
Removing -e parameter from else ribodetector (for single end)
brbergamo Apr 21, 2026
7af85df
Remove script parameter from ribodetector rule
mikemartinez99 Apr 21, 2026
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60 changes: 42 additions & 18 deletions .github/workflows/test.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,9 +6,9 @@ name: Snakemake_tests
on:
# Triggers the workflow on push or pull request events but only for the branches listed
push:
branches: [ master, dev-tim, dev-andrew-github-actions ]
branches: [ master, dev-tim, dev-andrew-github-actions, dev-ribodetector ]
pull_request:
branches: [ master, dev-tim, dev-andrew-github-actions ]
branches: [ master, dev-tim, dev-andrew-github-actions, dev-ribodetector ]

# Including this block the allow the workflow to be run manually from the GitHub Actions tab
workflow_dispatch:
Expand All @@ -29,12 +29,16 @@ jobs:
# Steps to be run
steps:
- uses: actions/checkout@v2
- name: Install Apptainer
uses: eWaterCycle/setup-apptainer@v2
with:
apptainer-version: 1.3.6
- name: Create_conda_env
uses: snakemake/snakemake-github-action@v1
with:
directory: '.'
snakefile: 'Snakefile'
args: '--cores 4 --use-conda --conda-create-envs-only'
args: '--cores 4 --use-conda --use-singularity --conda-create-envs-only'
- name: tar conda envs
run: |
tar -cf ./conda_envs_archive.tar ./.snakemake
Expand Down Expand Up @@ -88,26 +92,30 @@ jobs:

steps:
- uses: actions/checkout@v2
- name: Install Apptainer
uses: eWaterCycle/setup-apptainer@v2
with:
apptainer-version: 1.3.6
- name: Hisat_single_config_build
uses: snakemake/snakemake-github-action@v1
with:
directory: '.'
snakefile: 'Snakefile'
args: 'build_refs --cores 4 --use-conda --configfile tests/test_config_single_hisat.yaml'
args: 'build_refs --cores 4 --use-conda --use-singularity --configfile tests/test_config_single_hisat.yaml'
- name: Hisat_single_config_configure
run: cat ref/pipeline_refs/hg38_chr567_100k.entries.yaml >> tests/test_config_single_hisat.yaml
- name: Hisat_single_config_check
uses: snakemake/snakemake-github-action@v1
with:
directory: '.'
snakefile: 'Snakefile'
args: 'check_refs --cores 4 --use-conda --configfile tests/test_config_single_hisat.yaml'
args: 'check_refs --cores 4 --use-conda --use-singularity --configfile tests/test_config_single_hisat.yaml'
- name: Hisat_single_config_run
uses: snakemake/snakemake-github-action@v1
with:
directory: '.'
snakefile: 'Snakefile'
args: '--cores 4 --use-conda --configfile tests/test_config_single_hisat.yaml'
args: '--cores 4 --use-conda --use-singularity --configfile tests/test_config_single_hisat.yaml'

# paired_hisat
#
Expand All @@ -118,26 +126,30 @@ jobs:

steps:
- uses: actions/checkout@v2
- name: Install Apptainer
uses: eWaterCycle/setup-apptainer@v2
with:
apptainer-version: 1.3.6
- name: Hisat_paired_config_build
uses: snakemake/snakemake-github-action@v1
with:
directory: '.'
snakefile: 'Snakefile'
args: 'build_refs --cores 4 --use-conda --configfile tests/test_config_paired_hisat.yaml'
args: 'build_refs --cores 4 --use-conda --use-singularity --configfile tests/test_config_paired_hisat.yaml'
- name: Hisat_paired_config_configure
run: cat ref/pipeline_refs/hg38_chr567_100k.entries.yaml >> tests/test_config_paired_hisat.yaml
- name: Hisat_paired_config_check
uses: snakemake/snakemake-github-action@v1
with:
directory: '.'
snakefile: 'Snakefile'
args: 'check_refs --cores 4 --use-conda --configfile tests/test_config_paired_hisat.yaml'
args: 'check_refs --cores 4 --use-conda --use-singularity --configfile tests/test_config_paired_hisat.yaml'
- name: Hisat_paired_config_run
uses: snakemake/snakemake-github-action@v1
with:
directory: '.'
snakefile: 'Snakefile'
args: '--cores 4 --use-conda --configfile tests/test_config_paired_hisat.yaml'
args: '--cores 4 --use-conda --use-singularity --configfile tests/test_config_paired_hisat.yaml'

# single_star
#
Expand All @@ -147,26 +159,30 @@ jobs:

steps:
- uses: actions/checkout@v2
- name: Install Apptainer
uses: eWaterCycle/setup-apptainer@v2
with:
apptainer-version: 1.3.6
- name: STAR_single_config_build
uses: snakemake/snakemake-github-action@v1
with:
directory: '.'
snakefile: 'Snakefile'
args: 'build_refs --cores 4 --use-conda --configfile tests/test_config_single_star.yaml'
args: 'build_refs --cores 4 --use-conda --use-singularity --configfile tests/test_config_single_star.yaml'
- name: STAR_single_config_configure
run: cat ref/pipeline_refs/hg38_chr567_100k.entries.yaml >> tests/test_config_single_star.yaml
- name: STAR_single_config_check
uses: snakemake/snakemake-github-action@v1
with:
directory: '.'
snakefile: 'Snakefile'
args: 'check_refs --cores 4 --use-conda --configfile tests/test_config_single_star.yaml'
args: 'check_refs --cores 4 --use-conda --use-singularity --configfile tests/test_config_single_star.yaml'
- name: STAR_single_config_run
uses: snakemake/snakemake-github-action@v1
with:
directory: '.'
snakefile: 'Snakefile'
args: '--cores 4 --use-conda --configfile tests/test_config_single_star.yaml'
args: '--cores 4 --use-conda --use-singularity --configfile tests/test_config_single_star.yaml'

# paired_star
#
Expand All @@ -177,26 +193,30 @@ jobs:

steps:
- uses: actions/checkout@v2
- name: Install Apptainer
uses: eWaterCycle/setup-apptainer@v2
with:
apptainer-version: 1.3.6
- name: STAR_paired_config_build
uses: snakemake/snakemake-github-action@v1
with:
directory: '.'
snakefile: 'Snakefile'
args: 'build_refs --cores 4 --use-conda --configfile tests/test_config_paired_star.yaml'
args: 'build_refs --cores 4 --use-conda --use-singularity --configfile tests/test_config_paired_star.yaml'
- name: STAR_paired_config_configure
run: cat ref/pipeline_refs/hg38_chr567_100k.entries.yaml >> tests/test_config_paired_star.yaml
- name: STAR_paired_config_check
uses: snakemake/snakemake-github-action@v1
with:
directory: '.'
snakefile: 'Snakefile'
args: 'check_refs --cores 4 --use-conda --configfile tests/test_config_paired_star.yaml'
args: 'check_refs --cores 4 --use-conda --use-singularity --configfile tests/test_config_paired_star.yaml'
- name: STAR_paired_config_run
uses: snakemake/snakemake-github-action@v1
with:
directory: '.'
snakefile: 'Snakefile'
args: '--cores 4 --use-conda --configfile tests/test_config_paired_star.yaml'
args: '--cores 4 --use-conda --use-singularity --configfile tests/test_config_paired_star.yaml'

# paired_star with rsem
#
Expand All @@ -207,26 +227,30 @@ jobs:

steps:
- uses: actions/checkout@v2
- name: Install Apptainer
uses: eWaterCycle/setup-apptainer@v2
with:
apptainer-version: 1.3.6
- name: STAR_RSEM_paired_config_build
uses: snakemake/snakemake-github-action@v1
with:
directory: '.'
snakefile: 'Snakefile'
args: 'build_refs --cores 4 --use-conda --configfile tests/test_config_paired_star_rsem.yaml'
args: 'build_refs --cores 4 --use-conda --use-singularity --configfile tests/test_config_paired_star_rsem.yaml'
- name: STAR_RSEM_paired_config_configure
run: cat ref/pipeline_refs/hg38_chr567_100k.entries.yaml >> tests/test_config_paired_star_rsem.yaml
- name: STAR_RSEM_paired_config_check
uses: snakemake/snakemake-github-action@v1
with:
directory: '.'
snakefile: 'Snakefile'
args: 'check_refs --cores 4 --use-conda --configfile tests/test_config_paired_star_rsem.yaml'
args: 'check_refs --cores 4 --use-conda --use-singularity --configfile tests/test_config_paired_star_rsem.yaml'
- name: STAR_RSEM_paired_config_run
uses: snakemake/snakemake-github-action@v1
with:
directory: '.'
snakefile: 'Snakefile'
args: '--cores 4 --use-conda --configfile tests/test_config_paired_star_rsem.yaml'
args: '--cores 4 --use-conda --use-singularity --configfile tests/test_config_paired_star_rsem.yaml'

#debug_environment_info
#
Expand Down
19 changes: 19 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
@@ -0,0 +1,19 @@
.cache/*
.claude/*
.fontconfig/*
.snakemake/*
.Rapp.history
alignment/*
featurecounts/*
logs/*
markdup/*
metrics/*
multiqc_report_data/*
multiqc_report_plots/*
plots/*
qc/*
ribodetector/*
trimming/*
slurm_logs/*
*.log
multiqc_report.html
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