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Try to resolve intermittant conda-related CI failures #112

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merged 3 commits into from
Nov 11, 2024
Merged

Try to resolve intermittant conda-related CI failures #112

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5ba6c14
Remove defaults channel everywhere, put conda-forge first as is curre…
matthuska Nov 11, 2024
f975cf2
Add conda-forge to channel list for all envs
matthuska Nov 11, 2024
a92148c
Turn off fail-fast so we can see which tests can pass
matthuska Nov 11, 2024
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6 changes: 4 additions & 2 deletions .github/workflows/dryrun.yml
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
name: dry run CI
name: Dry run
on:
push:
branches:
Expand All @@ -7,6 +7,7 @@ on:
branches:
- main
- dev
workflow_dispatch:


env:
Expand All @@ -17,6 +18,7 @@ jobs:
name: Dry run ${{ matrix.inputtype }}-${{ matrix.profile }}-nf_${{ matrix.NXF_VER }} pipeline test
runs-on: ubuntu-latest
strategy:
fail-fast: false
matrix:
NXF_VER:
- "23.04.1"
Expand Down Expand Up @@ -61,7 +63,7 @@ jobs:
with:
auto-update-conda: true
conda-solver: libmamba
channels: conda-forge,bioconda,defaults
channels: conda-forge,bioconda
python-version: ${{ matrix.python-version }}

- name: Run nf-test
Expand Down
7 changes: 4 additions & 3 deletions envs/bbmap.yaml
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@@ -1,7 +1,8 @@
name: bbmap
channels:
- bioconda
- conda-forge
dependencies:
- bioconda
- nodefaults
dependencies:
- bbmap=38.79
- pigz=2.3.4
- pigz=2.3.4
7 changes: 4 additions & 3 deletions envs/bed_samtools.yaml
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@@ -1,7 +1,8 @@
name: bed+samtools
name: bed_samtools
channels:
- bioconda
- conda-forge
- bioconda
- nodefaults
dependencies:
- bedtools=2.30.0
- samtools=1.14
- samtools=1.14
7 changes: 4 additions & 3 deletions envs/bwa.yaml
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@@ -1,8 +1,9 @@
name: bwa
channels:
- bioconda
- conda-forge
dependencies:
- bioconda
- nodefaults
dependencies:
- bwa=0.7.18
- samtools=1.20
- htslib=1.20
- htslib=1.20
3 changes: 2 additions & 1 deletion envs/fastqc.yaml
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@@ -1,6 +1,7 @@
name: fastqc
channels:
- conda-forge
- bioconda
- nodefaults
dependencies:
- fastqc=0.11.9

3 changes: 2 additions & 1 deletion envs/minimap2.yaml
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@@ -1,7 +1,8 @@
name: minimap2
channels:
- bioconda
- conda-forge
- bioconda
- nodefaults
dependencies:
- minimap2=2.26
- samtools=1.17
Expand Down
3 changes: 2 additions & 1 deletion envs/multiqc.yaml
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@@ -1,7 +1,8 @@
name: multiqc
channels:
- conda-forge
- bioconda
- nodefaults
dependencies:
- python<3.12.0
- multiqc=1.12

3 changes: 2 additions & 1 deletion envs/nanoplot.yaml
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@@ -1,7 +1,8 @@
name: nanoplot
channels:
- bioconda
- conda-forge
- bioconda
- nodefaults
dependencies:
- nanoplot=1.32.1
- seaborn==0.10.1
Expand Down
4 changes: 3 additions & 1 deletion envs/pysam.yaml
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@@ -1,5 +1,7 @@
name: pysam
channels:
- conda-forge
- bioconda
- nodefaults
dependencies:
- pysam=0.19.1
- pysam=0.19.1
3 changes: 2 additions & 1 deletion envs/quast.yaml
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@@ -1,6 +1,7 @@
name: quast
channels:
- conda-forge
- bioconda
- nodefaults
dependencies:
- quast=5.0.2

5 changes: 3 additions & 2 deletions envs/samclipy.yaml
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@@ -1,7 +1,8 @@
name: samclipy
channels:
- bioconda
- conda-forge
- bioconda
- nodefaults
dependencies:
- samtools=1.11
- python=3.9.5
- python=3.9.5
3 changes: 2 additions & 1 deletion envs/seqkit.yaml
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@@ -1,7 +1,8 @@
name: seqkit
channels:
- bioconda
- conda-forge
- bioconda
- nodefaults
dependencies:
- seqkit==2.6.1
- tabix==1.11
Expand Down
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