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nf-core / differentialabundance

Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
https://nf-co.re/differentialabundance
MIT License
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Command error: .command.sh: line 3: gtf2featureAnnotation.R: command not found #224

Closed MustafaElshani closed 10 months ago

MustafaElshani commented 10 months ago

Description of the bug

When running the pipeline with gencode gtf, it seems to have the Command error: .command.sh: line 3: gtf2featureAnnotation.R: command not found error

Command used and terminal output

nextflow run nf-core/differentialabundance \
     --input samplesheet_input_DA.csv \
     --matrix nf-core_RNASEQ/star_salmon/salmon.merged.gene_counts.tsv \
     --transcript_length_matrix nf-core_RNASEQ/star_salmon/salmon.merged.gene_lengths.tsv \
     --contrasts contrast.csv \
     --gtf gencode.v41.primary_assembly.annotation.gtf \
     --gencode \
     -profile rnaseq, docker \
     --outdir ./differential_abundance

Relevant files

No response

System information

No response

MustafaElshani commented 10 months ago

This was solved with 

conda install bioconda::atlas-gene-annotation-manipulation