Commit cbb80dc4 authored by van den Berg's avatar van den Berg
Browse files

Add support for Snakemake 6.3.0

- Rename a variable named 'count' since that has become a reserved
  keyword in Snakemake.
- Remove tests for an exact version of Snakemake.
- Add a Changelog file.
parent 0bc60880
Changelog
==========
<!--
Newest changes should be on top.
This document is user facing. Please word the changes in such a way
that users understand how the changes affect the new version.
-->
v1.0.2-dev
---------------------------
+ Add support for Snakemake 6.3.0
......@@ -8,4 +8,4 @@ channels:
dependencies:
- pytest-workflow>=1.4.0
- python>3.6
- snakemake-minimal=5.9
- snakemake-minimal=6.3.0
......@@ -56,12 +56,12 @@ rule count_fragments:
bam="{sample}/snv-indels/{sample}.snv-indel.idsorted.bam",
gtf=settings["expression_gtf"],
output:
count="{sample}/expression/{sample}.fragments_per_gene",
fragments_per_gene="{sample}/expression/{sample}.fragments_per_gene",
threads: 1
singularity: containers["htseq"]
shell:
"htseq-count --format bam --order name --stranded no"
" {input.bam} {input.gtf} > {output.count}"
" {input.bam} {input.gtf} > {output.fragments_per_gene}"
rule count_raw_bases:
input:
......@@ -81,28 +81,28 @@ rule count_bases_exon:
raw="{sample}/expression/{sample}.raw_base",
aggr_script=settings["aggr_base_count_script"],
output:
count="{sample}/expression/{sample}.bases_per_exon",
bases_per_exon="{sample}/expression/{sample}.bases_per_exon",
params:
sample="{sample}"
threads: 1
singularity: containers["hamlet-scripts"]
shell:
"Rscript {input.aggr_script} -I {input.raw} -N {params.sample}"
" -E {output.count}"
" -E {output.bases_per_exon}"
rule count_bases_gene:
input:
raw="{sample}/expression/{sample}.raw_base",
aggr_script=settings["aggr_base_count_script"],
output:
count="{sample}/expression/{sample}.bases_per_gene",
bases_per_gene="{sample}/expression/{sample}.bases_per_gene",
params:
sample="{sample}"
threads: 1
singularity: containers["hamlet-scripts"]
shell:
"Rscript {input.aggr_script} -I {input.raw} -N {params.sample}"
" -G {output.count}"
" -G {output.bases_per_gene}"
rule calc_exon_ratios:
input:
......
......@@ -42,16 +42,6 @@
- "TestSample3/expression/TestSample3.fragments_per_gene"
- "TestSample3/expression/TestSample3.raw_base"
- name: test-expression-sanity-snakemake
tags:
- sanity
- expression
command: >
snakemake --version
stdout:
contains:
- "5.9"
- name: test-expression-sanity-singularity
tags:
- sanity
......
......@@ -68,16 +68,6 @@
- "TestSample3/fusion/TestSample3.sf-isect-circos/fsnviz.svg"
- "TestSample3/fusion/TestSample3.fusions-combined.svg"
- name: test-fusion-sanity-snakemake
tags:
- sanity
- fusion
command: >
snakemake --version
stdout:
contains:
- "5.9"
- name: test-fusion-sanity-singularity
tags:
- sanity
......
......@@ -40,16 +40,6 @@
- "TestSample3/hamlet_report.TestSample3.pdf"
- "TestSample3/TestSample3.summary.json"
- name: test-hamlet-sanity-snakemake
tags:
- sanity
- hamlet
command: >
snakemake --version
stdout:
contains:
- "5.9"
- name: test-hamlet-sanity-singularity
tags:
- sanity
......
......@@ -46,16 +46,6 @@
- "TestSample3/itd/TestSample3.flt3.bg.csv"
- "TestSample3/itd/TestSample3.flt3.png"
- name: test-itd-sanity-snakemake
tags:
- sanity
- itd
command: >
snakemake --version
stdout:
contains:
- "5.9"
- name: test-itd-sanity-singularity
tags:
- sanity
......
......@@ -22,16 +22,6 @@
contains:
- "Job counts:"
- name: test-qc-sanity-snakemake
tags:
- sanity
- qc
command: >
snakemake --version
stdout:
contains:
- "5.9"
- name: test-qc-sanity-singularity
tags:
- sanity
......
......@@ -36,16 +36,6 @@
- "TestSample3/snv-indels/TestSample3.variants_all.csv"
- "TestSample3/snv-indels/TestSample3.variants_hi.csv"
- name: test-snv-indels-sanity-snakemake
tags:
- sanity
- snv-indels
command: >
snakemake --version
stdout:
contains:
- "5.9"
- name: test-snv-indels-sanity-singularity
tags:
- sanity
......
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