add hic minimap2 #44
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add hic minimap2 #44
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workflows/genomeassembly.nf
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| GENOMESCOPE_MODEL( hifi_reads_ch ) | ||
| ch_versions = ch_versions.mix(GENOMESCOPE_MODEL.out.versions) | ||
| /*GENOMESCOPE_MODEL( hifi_reads_ch ) | ||
| ch_versions = ch_versions.mix(GENOMESCOPE_MODEL.out.versions)*/ |
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Was it commented out with the purpose of debugging and does it need uncommenting?
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yes, that was the purpose :) I will remove them now.
workflows/genomeassembly.nf
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| @@ -312,24 +312,27 @@ workflow GENOMEASSEMBLY { | |||
| GENOMESCOPE_MODEL.out.hist, | |||
| GENOMESCOPE_MODEL.out.ktab | |||
| ) | |||
| } | |||
| }*/ | |||
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Was it commented out with the purpose of debugging and does it need uncommenting?
workflows/genomeassembly.nf
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| @@ -347,7 +350,7 @@ workflow GENOMEASSEMBLY { | |||
| PREPARE_INPUT.out.busco, | |||
| GENOMESCOPE_MODEL.out.hist, | |||
| GENOMESCOPE_MODEL.out.ktab | |||
| ) | |||
| )*/ | |||
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Was it commented out with the purpose of debugging and does it need uncommenting?
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@yumisims Was this version of the pipeline tested on a big dataset with |
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@ksenia-krasheninnikova not necessary to test on a bigger genome. I encountered an image downloading problem, have you seen this before? |
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@yumisims what image exactly threw the error? Can't see it in the current CI run. As I understand the purpose of adding minimap2 option is to be able to run the pipeline on big genomes. |
gq1
reviewed
May 24, 2024
.github/workflows/ci.yml
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| @@ -38,6 +38,9 @@ jobs: | |||
| - name: Check out pipeline code | |||
| uses: actions/checkout@v3 | |||
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| - name: Setup apptainer | |||
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This step is already in this CI, duplicated.
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Check TreeVal to see how to run pipeline if you use nf-core download.
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@muffato do you know the reason why Container library: 'quay.io' is not valid? thanks |
gq1
reviewed
May 29, 2024
| container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | ||
| 'https://depot.galaxyproject.org/singularity/python:3' : | ||
| 'docker.io/python:3.9' }" |
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This container definition worked for nextflow run, probably not for nf-core download?
I tried to run the test on dev branch yesterday again without problems.
https://github.com/sanger-tol/genomeassembly/actions/runs/8988294821
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I can't see any difference with the Treeval CI and container definition.
On the farm, nf-core download works for me.
Or maybe a version incompatibility ? (e.g. different version of nf-core or apptainer/singularity or docker)
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That is what we discussed yesterday in the pipeline meeting.
Obviously -l flag didn't help. Now we can try to fix the nf-core version as the one on local.
ksenia-krasheninnikova
approved these changes
Jul 16, 2024
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PR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).