feat: qc rules #16
feat: qc rules #16
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…map + corresponding config/config.yml and profile/config.yml
workflow/Snakefile
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| shell: | ||
| "cat {input.samples} {input.mapping} >> QC-report.txt" | ||
| "tar zcvf {input}.tar.gz {input} 2> {log}" |
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Should this read tar zcvf {ouput} {input}? Also, &> {log} because there is no output stream (stdout and stderr) for which we do not want to gather in our log, right?
…hed qc rules from snakefile into their own .smk
.test/config-simple/config.yml
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| @@ -17,6 +17,8 @@ repo: "/~https://github.com/snakemake-workflows/transriptome-differential-expressi | |||
| transcriptome: "/lustre/miifs01/project/m2_zdvhpc/transcriptome_data/GCA_917627325.4_PGI_CHIRRI_v4_genomic.fa" | |||
| # Annotation GFF/GTF (absolute path) | |||
| annotation: "/lustre/miifs01/project/m2_zdvhpc/transcriptome_data/GCA_917627325.4_PGI_CHIRRI_v4_genomic.gff" | |||
| #gtf is needed by qualimap | |||
| gtf: "/lustre/miifs01/project/m2_zdvhpc/transcriptome_data/GCA_917627325.4_PGI_CHIRRI_v4_genomic.gtf" | |||
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please set a TODO-comment stating that we ought to evaluate just using the gtf version then: Basically both gff and gtf contain the same information and we should not require both, if one is sufficient.
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This is an artifact from previous versions which is only present in the /.test/config-simple/config.yml. Qualimap has since been removed from the workflow as running it with our .gtf file only returns warnings.
config/config.yml
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| @@ -19,6 +19,9 @@ transcriptome: "/lustre/miifs01/project/m2_zdvhpc/transcriptome_data/GCA_9176273 | |||
| annotation: "/lustre/miifs01/project/m2_zdvhpc/transcriptome_data/GCA_917627325.4_PGI_CHIRRI_v4_genomic.gff" | |||
| # these samples ought to contain all samples comprising of the | |||
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| #NanoPlot QC with sequencing summary. leave as None for QC with .fastq files | |||
| summary: None | |||
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this implicates the split between summary and non-summary evaluation. However, did we not want to have both, eventually?
workflow/Snakefile
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| @@ -3,6 +3,13 @@ from os import path | |||
| from collections import OrderedDict | |||
| import sys | |||
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| <<<<<<< HEAD | |||
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looks like an unresolved merge conflict (also see the lines below)
workflow/Snakefile
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| log: | ||
| "logs/NanoPlot/{sample}.log", | ||
| resources: | ||
| ## max of 39 for our SLURM partition | ||
| cpus_per_task= min(8,39) #problem with max(len(input.fastq),39) | ||
| cpus_per_task=min(8, 39), #problem with max(len(input.fastq),39) |
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cpus_per_task=min(len(input.fastq), config["max_cpus_in_default_partition/PC/
Server"])
vielleicht den Parameter anders nennen? ;-)
config/config.yml
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| @@ -19,6 +19,9 @@ transcriptome: "/lustre/miifs01/project/m2_zdvhpc/transcriptome_data/GCA_9176273 | |||
| annotation: "/lustre/miifs01/project/m2_zdvhpc/transcriptome_data/GCA_917627325.4_PGI_CHIRRI_v4_genomic.gff" | |||
| # these samples ought to contain all samples comprising of the | |||
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| # OPTIONAL; NanoPlot QC with summary from sequencer. leave as "None" for regular QC with .fastq files | |||
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Optional: NanoPlot QC summary using a summary file from the sequencer. If this file is not supplied, put the parameter to "None". It will then to an independent QC run per FASTQ input.
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| if config["summary"] == "None": | ||
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no empty line after if statement
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linting with snakefmt adds empty lines.
| "tar zcvf {output} {input} 2> {log}" | ||
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| else: | ||
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| "NanoPlot -t {resources.cpus_per_task} --tsv_stats -f svg " | ||
| "--fastq {input} -o {output} 2> {log}" | ||
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| rule compress_nplot: |
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should be a local rule, shouldn't it?
Added NanoPlot and Qualimap rules.