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* use small genomes to generate examples and stramline input definitions * corrected urls * relaxed allowed target name regex * stingency settings not ensembl specific, moved to main config * refactoring gtf/gff3 fileds def * major re-work of input staging and multitude of related changes * updated repr pep filtering * relaxed req to include supercontigs not just chromosomes * added sequencesToPlace spec to test config * restored core functionality after re-structure * cleanup, comments * added samtools container def * optional faidx process if idx no provided * added data set from non Esembl source * generalised gff3-based pep conversion to Ensembl style, also allows pass-through of already existing records * allowing user-specified chromosome id pattern for block and feature JSON generation * updated and documented test data sets * travis stub * opted for smaller samtools container * hack to handle gz (not bgz) files fro chr lengths * minor * Update README.md * Update .travis.yaml * Update .travis.yaml * Update .travis.yaml * Update .travis.yaml * test profile with local data * travis data download and untar * travis fixes * ubu version for travis * updated dep * for GH actions * docker user change for GH actions * docker groovy test for GHA * docker user * docker grp exists * added go for singularity * added groovy image with ps * reconf * test profile updates - fix for groovy @grab failing with singularity (read only file-system) - fix errorStrategy config * added Singularity install to GH actions * Singularity dependencies @ GH actions * working around https://github.com/sylabs/singularity/issues/3634 * test singularity pull form docker * explicit use of gawk - may matter on alpine * workaround for nextflow-io/nextflow#1210 sylabs/singularity#3634 * leaner fastx container * fastx and reconf * fix path to script, renamed tasks * test wspace path * added missing script, fixed GH actions cmd * ansi-lo on and try docker again * docker workflow test * fix typo * fix typo * fix for permission denied GH actions (?) * fix for groovy grapes in docker * test * test * test * test * another docker test * GH A job.needs experiemnt * GH A tidy * GH A fix indent * GH A fix job * added GH actions CI badge * re-implemented: duplicate emissions if multiple annotations per reference assembly * updated datastes in line with feature dev * another badge ver * fix * added EP datasets * ensure non-empty process out * generalised for different gff3 interpretations * Delete .travis.yaml * Update README.md * Update README.md * At & Bd ref fasta not needed * speeding things up: gawk in jq container and up resources * do not report markers placed outside pseudochromosomes (e.g. on scaffolds) * id pattern match extended to seq placement * redundant-ish * added TOC
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,68 @@ | ||
| name: CI | ||
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| on: [push] | ||
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| jobs: | ||
| docker: | ||
| runs-on: ubuntu-18.04 | ||
| steps: | ||
| - name: Install GraphViz | ||
| run: | | ||
| sudo apt-get update && sudo apt-get install -y graphviz | ||
| - name: Install Nextflow | ||
| run: | | ||
| wget -qO- get.nextflow.io | bash | ||
| sudo mv nextflow /usr/local/bin/ | ||
| - name: Check out code | ||
| uses: actions/checkout@v1 | ||
| - name: Test workflow (docker) | ||
| run: | | ||
| NXF_VER=19.10.0 nextflow run ${GITHUB_WORKSPACE} -profile CI,docker --max_cpus 2 --max_memory 4.GB -ansi-log false | ||
| singularity: | ||
| runs-on: ubuntu-18.04 | ||
| # runs-on: ubuntu-18.04 | ||
| steps: | ||
| - name: Check out code | ||
| uses: actions/checkout@v1 | ||
| - name: Set up Go | ||
| uses: actions/setup-go@v1 | ||
| with: | ||
| go-version: 1.13 | ||
| id: go | ||
| - name: Install Dependencies for Singularity | ||
| run: | | ||
| sudo apt-get update && sudo apt-get install -y \ | ||
| build-essential \ | ||
| libssl-dev \ | ||
| uuid-dev \ | ||
| libgpgme11-dev \ | ||
| squashfs-tools \ | ||
| libseccomp-dev \ | ||
| pkg-config | ||
| - name: Install Singularity | ||
| env: | ||
| SINGULARITY_VERSION: 3.5.2 | ||
| run: | | ||
| export GOPATH=/tmp/go | ||
| mkdir -p $GOPATH | ||
| sudo mkdir -p /usr/local/var/singularity/mnt && \ | ||
| mkdir -p $GOPATH/src/github.com/sylabs && \ | ||
| cd $GOPATH/src/github.com/sylabs && \ | ||
| wget -qO- https://github.com/sylabs/singularity/releases/download/v${SINGULARITY_VERSION}/singularity-${SINGULARITY_VERSION}.tar.gz | \ | ||
| tar xzv && \ | ||
| cd singularity && \ | ||
| ./mconfig -p /usr/local && \ | ||
| make -C builddir && \ | ||
| sudo make -C builddir install | ||
| - name: Install Nextflow | ||
| run: | | ||
| wget -qO- get.nextflow.io | bash | ||
| sudo mv nextflow /usr/local/bin/ | ||
| - name: Pull containers | ||
| run: | | ||
| echo "GITHUB_WORKSPACE: ${GITHUB_WORKSPACE}" | ||
| nextflow run ${GITHUB_WORKSPACE}/pull_containers.nf -ansi-log false -profile singularity | ||
| - name: Test workflow (singularity) | ||
| run: | | ||
| NXF_VER=19.10.0 nextflow run ${GITHUB_WORKSPACE} -profile CI,singularity --max_cpus 2 --max_memory 4.GB -ansi-log false |
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| Original file line number | Diff line number | Diff line change |
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| @@ -1,4 +1,4 @@ | ||
| #!/usr/bin/awk -f | ||
| #!/usr/bin/gawk -f | ||
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| BEGIN { | ||
| FS="\t"; | ||
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