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.

CHANGELOG.md

+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

environment.yml

@@ -8,4 +8,4 @@ channels:
 dependencies:
  - pytest-workflow>=1.4.0
  - python>3.6
- - snakemake-minimal=5.9
+ - snakemake-minimal=6.3.0

includes/expression/Snakefile

@@ -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:

test/test_expression.yml

@@ -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

test/test_fusion.yml

@@ -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

test/test_hamlet.yml

@@ -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

test/test_itd.yml

@@ -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

test/test_qc_seq.yml

@@ -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

test/test_snv_indels.yml

@@ -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