When I run the workflow I get the following error:
$ snakemake --cores 12 --use-conda
Workflow defines that rule get_genome is eligible for caching between workflows (use the --cache argument to enable this).
Workflow defines that rule get_annotation is eligible for caching between workflows (use the --cache argument to enable this).
Workflow defines that rule genome_faidx is eligible for caching between workflows (use the --cache argument to enable this).
Workflow defines that rule bwa_index is eligible for caching between workflows (use the --cache argument to enable this).
Workflow defines that rule star_index is eligible for caching between workflows (use the --cache argument to enable this).
Assuming unrestricted shared filesystem usage.
Building DAG of jobs...
MissingInputException in rule count_matrix in file https://raw.githubusercontent.com/snakemake-workflows/rna-seq-star-deseq2/v2.1.2/workflow/rules/diffexp.smk, line 1:
Missing input files for rule count_matrix:
output: results/counts/all.tsv
affected files:
results/star/Sample12_lane1/ReadsPerGene.out.tab
results/star/Sample2_lane1/ReadsPerGene.out.tab
results/star/Sample10_lane1/ReadsPerGene.out.tab
results/star/Sample4_lane2/ReadsPerGene.out.tab
results/star/Sample15_lane1/ReadsPerGene.out.tab
results/star/Sample6_lane1/ReadsPerGene.out.tab
results/star/Sample13_lane1/ReadsPerGene.out.tab
results/star/Sample8_lane1/ReadsPerGene.out.tab
results/star/Sample17_lane1/ReadsPerGene.out.tab
Could anyone help me understand how to resolve this issue?
I am trying to run paired end reads of mouse fastq files. Im not sure how to resolve the error that i keep getting. My config.yml:
When I run the workflow I get the following error:
Could anyone help me understand how to resolve this issue?