rnaseq
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nf-core
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
### Description of feature Is there any plan to add WGCNA to the workflow? Thanks.
## PR checklist - [x] This comment contains a description of changes (with reason). digging into #855 more on our side, we found that the .nextflow.log contained the error: >...
Hi, I noticed that the `-g` parameter of the `ext.args` in the `SUBREAD_FEATURECOUNTS` process is not set correctly when passing the `gencode` parameter via a config file e.g. `-c my_rnaseq.config`....
### Description of the bug Run stops without results generated or indication of why it didn't finish. ### Command used and terminal output ```console nextflow run nf-core/rnaseq --input pisumSRRs/samplesheet/samplesheet.csv --outdir...
`console` snippets are in general only nice to display terminal outputs, not anything related to scripts or commands. ## PR checklist - [x] This comment contains a description of changes...
### Description of the bug Ref: https://github.com/gpertea/stringtie Missing XS tag from STAR. bam file Header: @PG ID:STAR PN:STAR VN:STAR_2.6.1d CL:STAR --runThreadN 12 --runRNGseed 0 --genomeDir STARIndex --readFilesIn EngTreg2_1_1_val_1.fq.gz EngTreg2_1_2_val_2.fq.gz --readFilesCommand...
Using the default settings I ran into the issue of the `fastqc` wrapper of `trim_galore` did not pass in the threads from the process into the fastqc substep. As a...
### Description of the bug Running rnaseq -r 3.8.1 with -profile docker on a local machine gives this strange error that has me stumped. "Too many levels of symbolic links"...
### Description of the bug I am trying to run nf-core with RSEM to quantify gene expression. However, the process RSEM calculate expression fails and exits with error code 255....
### Description of the bug On version 3.8.1, I have run into an issue where the pipeline runs entirely without issue through the final multiqc step, but fails at the...
