Error: "An output file is marked as pipe, but consuming jobs are part of conflicting groups."

[Rubbert]

Hi @aryarm ,

I am running your pipeline starting with called peaks and a .BAM file. However, when doing a dry-run, I get the following error:

"Building DAG of jobs... WorkflowError in line 350 of /home/######/projects/varCA/rules/prepare.smk: An output file is marked as pipe, but consuming jobs are part of conflicting groups."

My sample.tsv file looks like:

EMC378 /absPathTo/EMC378.filtered.bam /absPathTo/EMC378_peaks.bed EMC385 /absPathTo/EMC385.filtered.bam /absPathTo/EMC385_peaks.bed ....

In my config.yaml I define:

sample_file: /absPathTo/BSF_1013_2000HIV_hg38_perIndiv_atac_varCA_samples.tsv
genome: /absPathTo/genome.fa
snp_callers: [gatk-snp, varscan-snp, vardict-snp]
indel_callers: [gatk-indel, varscan-indel, vardict-indel, pindel, illumina-strelka]
snp_filter: ['gatk-snp~DP>5']
indel_filter: ['gatk-indel~DP>5']
snp_model: data/snp.rda
indel_model: data/indel.rda

I cloned your repository on Jul 26 13:11. I am running Snakemake 6.6.0

I run the following command to do a dry-run: snakemake --config out="$out_path" -p -n

I might have misunderstood something in the way different folders need to be defined, so apologies in advance if that is the case.

Thanks!

PS. Could it be that the example data is no longer available?