fix: update samtools.yaml to latest 1.17 and update github actions (#…

…75)

@manuelphilip Was there a reason for the old version of `samtools =1.9`?
Otherwise I would update this to the latest version.

I found this, because we were seeing very large memory usage (`> 20GB`)
for the `rule get_mapped_canonical_transcripts`, which should stream
through the BAM (and the BAMs we had were below `1GB`), so I wouldn't
expect any large memory usage. The only explanation I have so far, is
that maybe this very old version of samtools somehow had a bug or very
suboptimal handling of BAM files.

.github/workflows/main.yml

@@ -41,9 +41,9 @@ jobs:
  formatting:
  runs-on: ubuntu-latest
  steps:
- - uses: actions/checkout@v1
+ - uses: actions/checkout@v3
  - name: Formatting
- uses: github/super-linter@v4
+ uses: github/super-linter@v5
  env:
  VALIDATE_ALL_CODEBASE: false
  DEFAULT_BRANCH: main
@@ -52,9 +52,9 @@ jobs:
  linting:
  runs-on: ubuntu-latest
  steps:
- - uses: actions/checkout@v1
+ - uses: actions/checkout@v3
  - name: Linting
- uses: snakemake/snakemake-github-action@v1.22.0
+ uses: snakemake/snakemake-github-action@v1
  with:
  directory: .test
  snakefile: workflow/Snakefile
@@ -68,12 +68,12 @@ jobs:
  steps:
 
  - name: Checkout repository
- uses: actions/checkout@v2
+ uses: actions/checkout@v3
  with:
  submodules: recursive
 
  - name: Test workflow
- uses: snakemake/snakemake-github-action@v1.23.0
+ uses: snakemake/snakemake-github-action@v1
  with:
  directory: .test
  snakefile: workflow/Snakefile
@@ -87,12 +87,12 @@ jobs:
  steps:
 
  - name: Checkout repository
- uses: actions/checkout@v2
+ uses: actions/checkout@v3
  with:
  submodules: recursive
 
  - name: Test 3-prime-workflow
- uses: snakemake/snakemake-github-action@v1.23.0
+ uses: snakemake/snakemake-github-action@v1
  with:
  directory: .test/3-prime-config
  snakefile: workflow/Snakefile
@@ -101,7 +101,7 @@ jobs:
  # TODO: add some kind of test mode to report generation which does not really try to include
  # results.
  # - name: Test report
- # uses: snakemake/snakemake-github-action@v1.22.0
+ # uses: snakemake/snakemake-github-action@v1
  # with:
  # directory: .test
  # snakefile: workflow/Snakefile

workflow/envs/samtools.yaml

@@ -4,4 +4,4 @@ channels:
  - nodefaults
 
 dependencies:
- - samtools =1.9
+ - samtools =1.17