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multiqc update
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tdayris committed Feb 21, 2024
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14 changes: 7 additions & 7 deletions .github/workflows/main.yaml
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Expand Up @@ -49,10 +49,10 @@ jobs:
with:
directory: .test
snakefile: workflow/Snakefile
args: "--use-conda --use-singularity --show-failed-logs --cores 2 --conda-cleanup-pkgs cache"
# - name: Test report
# uses: snakemake/[email protected]
# with:
# directory: .test
# snakefile: workflow/Snakefile
# args: "--use-conda --use-singularity --cores 2 --report report.zip"
args: "--software-deployment-method conda --show-failed-logs --cores 2 --conda-cleanup-pkgs cache"
- name: Test report
uses: snakemake/[email protected]
with:
directory: .test
snakefile: workflow/Snakefile
args: "--software-deployment-method conda --cores 2 --report report.zip"
1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -8,6 +8,7 @@
* Relies on fair_genome_indexer version 3.1.4
* Relies on fair_bowtie2_mapping version 3.1.0
* Relies on fair_fastqc_multiqc version 2.0.3
* MultiQC now holds only one `{species}.{build}.{release}`

## Fixes:

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48 changes: 24 additions & 24 deletions README.md
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Expand Up @@ -26,16 +26,16 @@ The tools used in this pipeline are described [here](https://github.com/tdayris/

| Step | Commands |
| -------------------------------- | ---------------------------------------------------------------------------------------------------------------- |
| Download DNA Fasta from Ensembl | [ensembl-sequence](https://snakemake-wrappers.readthedocs.io/en/v3.3.3/wrappers/reference/ensembl-sequence.html) |
| Download DNA Fasta from Ensembl | [ensembl-sequence](https://snakemake-wrappers.readthedocs.io/en/v3.3.6/wrappers/reference/ensembl-sequence.html) |
| Remove non-canonical chromosomes | [pyfaidx](https://github.com/mdshw5/pyfaidx) |
| Index DNA sequence | [samtools](https://snakemake-wrappers.readthedocs.io/en/v3.3.3/wrappers/samtools/faidx.html) |
| Creatse sequence Dictionary | [picard](https://snakemake-wrappers.readthedocs.io/en/v3.3.3/wrappers/picard/createsequencedictionary.html) |
| Index DNA sequence | [samtools](https://snakemake-wrappers.readthedocs.io/en/v3.3.6/wrappers/samtools/faidx.html) |
| Creatse sequence Dictionary | [picard](https://snakemake-wrappers.readthedocs.io/en/v3.3.6/wrappers/picard/createsequencedictionary.html) |

#### Get genome annotation (GTF)

| Step | Commands |
| ---------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------- |
| Download GTF annotation | [ensembl-annotation](https://snakemake-wrappers.readthedocs.io/en/v3.3.3/wrappers/reference/ensembl-annotation.html) |
| Download GTF annotation | [ensembl-annotation](https://snakemake-wrappers.readthedocs.io/en/v3.3.6/wrappers/reference/ensembl-annotation.html) |
| Fix format errors | [Agat](https://agat.readthedocs.io/en/latest/tools/agat_convert_sp_gff2gtf.html) |
| Remove non-canonical chromosomes, based on above DNA Fasta | [Agat](https://agat.readthedocs.io/en/latest/tools/agat_sq_filter_feature_from_fasta.html) |
| Remove `<NA>` Transcript support levels | [Agat](https://agat.readthedocs.io/en/latest/tools/agat_sp_filter_feature_by_attribute_value.html) |
Expand All @@ -44,32 +44,32 @@ The tools used in this pipeline are described [here](https://github.com/tdayris/

| Step | Commands |
| -------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------- |
| Download dbSNP variants | [ensembl-variation](https://snakemake-wrappers.readthedocs.io/en/v3.3.3/wrappers/reference/ensembl-variation.html) |
| Filter non-canonical chromosomes | [pyfaidx](https://github.com/mdshw5/pyfaidx) + [BCFTools](https://snakemake-wrappers.readthedocs.io/en/v3.3.3/wrappers/bcftools/filter.html) |
| Index variants | [tabix](https://snakemake-wrappers.readthedocs.io/en/v3.3.3/wrappers/tabix/index.html) |
| Download dbSNP variants | [ensembl-variation](https://snakemake-wrappers.readthedocs.io/en/v3.3.6/wrappers/reference/ensembl-variation.html) |
| Filter non-canonical chromosomes | [pyfaidx](https://github.com/mdshw5/pyfaidx) + [BCFTools](https://snakemake-wrappers.readthedocs.io/en/v3.3.6/wrappers/bcftools/filter.html) |
| Index variants | [tabix](https://snakemake-wrappers.readthedocs.io/en/v3.3.6/wrappers/tabix/index.html) |

### Bowtie2 Mapping with [`fair_bowtie2_mapping`](https://github.com/tdayris/fair_bowtie2_mapping/tree/main)

#### Align reads over the genome

| Step | Meta-Wrapper | Wrapper |
| ---------------- | ------------------------------------------------------------------------------------------------------------------------ | -------------------------------------------------------------------------------------------------------------------------------- |
| Bowtie2-build | [bowtie2-sambamba meta-wrapper](https://snakemake-wrappers.readthedocs.io/en/v3.3.3/meta-wrappers/bowtie2_sambamba.html) | [bowtie2-build](https://snakemake-wrappers.readthedocs.io/en/v3.3.3/wrappers/bowtie2/build.html) |
| Bowtie2-build | [bowtie2-sambamba meta-wrapper](https://snakemake-wrappers.readthedocs.io/en/v3.3.6/meta-wrappers/bowtie2_sambamba.html) | [bowtie2-build](https://snakemake-wrappers.readthedocs.io/en/v3.3.6/wrappers/bowtie2/build.html) |
| Fastp | | [fastp](https://snakemake-wrappers.readthedocs.io/en/stable/wrappers/fastp.html) |
| Bowtie2-align | [bowtie2-sambamba meta-wrapper](https://snakemake-wrappers.readthedocs.io/en/v3.3.3/meta-wrappers/bowtie2_sambamba.html) | [bowtie2-align](https://snakemake-wrappers.readthedocs.io/en/v3.3.3/wrappers/bowtie2/align.html) |
| Sambamba sort | [bowtie2-sambamba meta-wrapper](https://snakemake-wrappers.readthedocs.io/en/v3.3.3/meta-wrappers/bowtie2_sambamba.html) | [sambamba-sort](https://snakemake-wrappers.readthedocs.io/en/v3.3.3/wrappers/sambamba/sort.html) |
| Sambamba-view | [bowtie2-sambamba meta-wrapper](https://snakemake-wrappers.readthedocs.io/en/v3.3.3/meta-wrappers/bowtie2_sambamba.html) | [sambamba-view](https://snakemake-wrappers.readthedocs.io/en/v3.3.3/wrappers/sambamba/view.html) |
| Sambamba-markdup | [bowtie2-sambamba meta-wrapper](https://snakemake-wrappers.readthedocs.io/en/v3.3.3/meta-wrappers/bowtie2_sambamba.html) | [sambamba-markdup](https://snakemake-wrappers.readthedocs.io/en/v3.3.3/wrappers/sambamba/markdup.html) |
| Sambamba-index | [bowtie2-sambamba meta-wrapper](https://snakemake-wrappers.readthedocs.io/en/v3.3.3/meta-wrappers/bowtie2_sambamba.html) | [sambamba-index](https://snakemake-wrappers.readthedocs.io/en/v3.3.3/wrappers/sambamba/index.html) |
| Bowtie2-align | [bowtie2-sambamba meta-wrapper](https://snakemake-wrappers.readthedocs.io/en/v3.3.6/meta-wrappers/bowtie2_sambamba.html) | [bowtie2-align](https://snakemake-wrappers.readthedocs.io/en/v3.3.6/wrappers/bowtie2/align.html) |
| Sambamba sort | [bowtie2-sambamba meta-wrapper](https://snakemake-wrappers.readthedocs.io/en/v3.3.6/meta-wrappers/bowtie2_sambamba.html) | [sambamba-sort](https://snakemake-wrappers.readthedocs.io/en/v3.3.6/wrappers/sambamba/sort.html) |
| Sambamba-view | [bowtie2-sambamba meta-wrapper](https://snakemake-wrappers.readthedocs.io/en/v3.3.6/meta-wrappers/bowtie2_sambamba.html) | [sambamba-view](https://snakemake-wrappers.readthedocs.io/en/v3.3.6/wrappers/sambamba/view.html) |
| Sambamba-markdup | [bowtie2-sambamba meta-wrapper](https://snakemake-wrappers.readthedocs.io/en/v3.3.6/meta-wrappers/bowtie2_sambamba.html) | [sambamba-markdup](https://snakemake-wrappers.readthedocs.io/en/v3.3.6/wrappers/sambamba/markdup.html) |
| Sambamba-index | [bowtie2-sambamba meta-wrapper](https://snakemake-wrappers.readthedocs.io/en/v3.3.6/meta-wrappers/bowtie2_sambamba.html) | [sambamba-index](https://snakemake-wrappers.readthedocs.io/en/v3.3.6/wrappers/sambamba/index.html) |

#### Quality controls

| Step | Wrapper |
| -------- | -------------------------------------------------------------------------------------------------------------------------------- |
| Picard | [picard-collectmultiplemetrics](https://snakemake-wrappers.readthedocs.io/en/stable/wrappers/picard/collectmultiplemetrics.html) |
| Samtools | [samtools-stats](https://snakemake-wrappers.readthedocs.io/en/v3.3.3/wrappers/samtools/stats.html) |
| FastQC | [fastqc-wrapper](https://snakemake-wrappers.readthedocs.io/en/v3.3.3/wrappers/fastqc.html) |
| MultiQC | [multiqc-wrapper](https://snakemake-wrappers.readthedocs.io/en/v3.3.3/wrappers/multiqc.html) |
| Samtools | [samtools-stats](https://snakemake-wrappers.readthedocs.io/en/v3.3.6/wrappers/samtools/stats.html) |
| FastQC | [fastqc-wrapper](https://snakemake-wrappers.readthedocs.io/en/v3.3.6/wrappers/fastqc.html) |
| MultiQC | [multiqc-wrapper](https://snakemake-wrappers.readthedocs.io/en/v3.3.6/wrappers/multiqc.html) |


### Call variants with Mutect2
Expand All @@ -78,17 +78,17 @@ The tools used in this pipeline are described [here](https://github.com/tdayris/

| Step | Meta-Wrapper | Wrapper |
| ----------------------------------- | -------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------- |
| Per-sample annotation | [GATK short variant calling](https://snakemake-wrappers.readthedocs.io/en/v3.3.3/meta-wrappers/gatk_mutect2_calling.html) | [add-or-replace-groups](https://snakemake-wrappers.readthedocs.io/en/v3.3.3/wrappers/picard/addorreplacereadgroups.html) |
| Mutect2 calling | [GATK short variant calling](https://snakemake-wrappers.readthedocs.io/en/v3.3.3/meta-wrappers/gatk_mutect2_calling.html) | [mutect2](https://snakemake-wrappers.readthedocs.io/en/v3.3.3/wrappers/gatk/mutect.html) |
| Infer contaminations | [GATK short variant calling](https://snakemake-wrappers.readthedocs.io/en/v3.3.3/meta-wrappers/gatk_mutect2_calling.html) | [get-pileup-summaries](https://snakemake-wrappers.readthedocs.io/en/v3.3.3/wrappers/gatk/getpileupsummaries.html) |
| Estimate corss-sample contamination | [GATK short variant calling](https://snakemake-wrappers.readthedocs.io/en/v3.3.3/meta-wrappers/gatk_mutect2_calling.html) | [calculate-contamination](https://snakemake-wrappers.readthedocs.io/en/v3.3.3/wrappers/gatk/calculatecontamination.html) |
| Search for sequencing artifact bias | [GATK short variant calling](https://snakemake-wrappers.readthedocs.io/en/v3.3.3/meta-wrappers/gatk_mutect2_calling.html) | [learn-read-orientation-model](https://snakemake-wrappers.readthedocs.io/en/v3.3.3/wrappers/gatk/learnreadorientationmodel.html) |
| Filtering calls | [GATK short variant calling](https://snakemake-wrappers.readthedocs.io/en/v3.3.3/meta-wrappers/gatk_mutect2_calling.html) | [filter-mutect-calls](https://snakemake-wrappers.readthedocs.io/en/v3.3.3/wrappers/gatk/filtermutectcalls.html) |
| Per-sample annotation | [GATK short variant calling](https://snakemake-wrappers.readthedocs.io/en/v3.3.6/meta-wrappers/gatk_mutect2_calling.html) | [add-or-replace-groups](https://snakemake-wrappers.readthedocs.io/en/v3.3.6/wrappers/picard/addorreplacereadgroups.html) |
| Mutect2 calling | [GATK short variant calling](https://snakemake-wrappers.readthedocs.io/en/v3.3.6/meta-wrappers/gatk_mutect2_calling.html) | [mutect2](https://snakemake-wrappers.readthedocs.io/en/v3.3.6/wrappers/gatk/mutect.html) |
| Infer contaminations | [GATK short variant calling](https://snakemake-wrappers.readthedocs.io/en/v3.3.6/meta-wrappers/gatk_mutect2_calling.html) | [get-pileup-summaries](https://snakemake-wrappers.readthedocs.io/en/v3.3.6/wrappers/gatk/getpileupsummaries.html) |
| Estimate corss-sample contamination | [GATK short variant calling](https://snakemake-wrappers.readthedocs.io/en/v3.3.6/meta-wrappers/gatk_mutect2_calling.html) | [calculate-contamination](https://snakemake-wrappers.readthedocs.io/en/v3.3.6/wrappers/gatk/calculatecontamination.html) |
| Search for sequencing artifact bias | [GATK short variant calling](https://snakemake-wrappers.readthedocs.io/en/v3.3.6/meta-wrappers/gatk_mutect2_calling.html) | [learn-read-orientation-model](https://snakemake-wrappers.readthedocs.io/en/v3.3.6/wrappers/gatk/learnreadorientationmodel.html) |
| Filtering calls | [GATK short variant calling](https://snakemake-wrappers.readthedocs.io/en/v3.3.6/meta-wrappers/gatk_mutect2_calling.html) | [filter-mutect-calls](https://snakemake-wrappers.readthedocs.io/en/v3.3.6/wrappers/gatk/filtermutectcalls.html) |


#### Quality controls

| Step | Wrapper |
| ------------------ | -------------------------------------------------------------------------------------------------- |
| Variant Evaluation | [variant-eval](https://snakemake-wrappers.readthedocs.io/en/v3.3.3/wrappers/gatk/varianteval.html) |
| MultiQC | [multiqc-wrapper](https://snakemake-wrappers.readthedocs.io/en/v3.3.3/wrappers/multiqc.html) |
| Variant Evaluation | [variant-eval](https://snakemake-wrappers.readthedocs.io/en/v3.3.6/wrappers/gatk/varianteval.html) |
| MultiQC | [multiqc-wrapper](https://snakemake-wrappers.readthedocs.io/en/v3.3.6/wrappers/multiqc.html) |
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