Release PR for 2.1.0 #197
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Release PR for 2.1.0 #197
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Add parameters to allow the use of MirGeneDB as database in the smranseq pipeline. The paths to the files are still temporary.
Added a if statement to assign the new mature and hairpin fasta files if MirGeneDB is to be used in the analysis.
Added the option to use the mirGeneDB species to parse the fasta files as different styles in species naming result in mis-parsed files.
Commit of the latest testing changes
Enable the use of the mirGeneDB gff file in the mirtop analysis and replace the mirna_gtf file with it internally.
Added a new variable that either takes the mirGeneDB or the mirtrace species to filter the fasta files.
Add the new options and their description to the schema.
Moved the devinition of the filterSpecies variable to the smrnaseq workflow instead of the individual modules.
Added the decoumentation of new parameters and features to the appropriate files.
This commit adds three modules to filter conatminants from the smRNA-Seq data. Using databses provided by the user the reads are filtered for rrna, trna, cdna, ncrna, and pirna. The provided files are filtered to remove miRNAs, indexed and used as reference to map the reads to using bowtie2. Reads that map to a contaminant database are removed from the sample. The process is optional and only those contaminants will be filtered for which a reference database has been provided.
Adds a workflow to run the contamination filtering processes introduced by an earlier commit.
Adds the contamination filtering subworkflow into the existing pipeline.
The added process collects the contamination filtering statistics and combines them to be added to the MultiQC output.
Added the FILTER_STATS step and the necessary alterations to hand over the data to the new process.
Enables the process to access all required stats files of each sample for processing.
Removed the appended filter tags and changed the naming of the individual stats files to be better accessible downstream
Altered the statistics output to be in line with the format for custom multiQC plots. In addition the number of remaining reads is now included in the statistics.
Changed the output file name and adjusted the awk output to be readable by multiQC.
Added an additional filter step that can be used to filter with a custom database in addition to the other databases.
Added the contamination filtering statistics to the multiqc output.
Added the options and default settings to filter contamination from the supplied sequence files. By default contamination filtering is disabled.
Added the new options to the nextflow_schema.
Changed the output of the contamination step to be gzipped.
Moved the enabeling command for contaminaition filtering to the top of hte section.
Add FastA of known adapters
Update changelog for 2.1.0 release, add config changes and update module
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JoseEspinosa
approved these changes
Oct 20, 2022
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
Joses comments resolved for release
edmundmiller
approved these changes
Oct 24, 2022
Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>
Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>
Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>
Shameless self merge as this is only reviewers comments :-)
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PR for upcoming release 2.1.0
PR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).