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Commit 2e59f7e1 authored by Sander Bollen's avatar Sander Bollen
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fix collectstats contianer

parent 08d2bb1c
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Pipeline #2616 failed
......@@ -588,7 +588,7 @@ rule fastqc_stats:
postqc_r1="{sample}/pre_process/postqc_fastqc/{sample}.cutadapt_R1_fastqc.zip",
postqc_r2="{sample}/pre_process/postqc_fastqc/{sample}.cutadapt_R2_fastqc.zip",
sc=fqpy
singularity: "docker://quay.io/biocontainers/vtools:1.0.0--py37h3010b51_0"
singularity: "docker://python:3.6-slim"
conda: "envs/collectstats.yml"
output:
"{sample}/pre_process/fastq_stats.json"
......@@ -664,7 +664,7 @@ if len(BASE_BEDS) >= 1:
fthresh=FEMALE_THRESHOLD
output:
"{sample}/{sample}.stats.json"
singularity: "docker://python:3.6-slim"
singularity: "docker://quay.io/biocontainers/vtools:1.0.0--py37h3010b51_0"
conda: "envs/collectstats.yml"
shell: "python {input.colpy} --sample-name {params.sample_name} "
"--pre-qc-fastq {input.preqc} --post-qc-fastq {input.postq} "
......@@ -689,7 +689,7 @@ else:
fthresh = FEMALE_THRESHOLD
output:
"{sample}/{sample}.stats.json"
singularity: "docker://python:3.6-slim"
singularity: "docker://quay.io/biocontainers/vtools:1.0.0--py37h3010b51_0"
conda: "envs/collectstats.yml"
shell: "python {input.colpy} --sample-name {params.sample_name} "
"--pre-qc-fastq {input.preqc} --post-qc-fastq {input.postq} "
......
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