https://nf-co.re logo
Join Slack
Powered by
I see some issue with the `dowload` part of the CI...
# tools
m
I see some issue with the 
dowload
part of the CI in a dev to master release: https://github.com/nf-core/rnavar/actions/runs/18676421290/job/53247266997?pr=248 template is up to date with latest
any idea @Júlia Mir?
m
What do you get if you run nextflow inspect manually?
j
@Julian Flesch and I found a possible problem, Nextflow is now printing a "Pipeline is starting" and "Pipeline complete" with 
nextflow inspect
so the output is not pure json anymore
party this 1
I would say Nextflow has to fix this, when we specify 
-format json
we shouldn't see any extra text
what do you think?
m
Ooooh
I see that's due to the experiment with #C08TKFDUNHG
j
Copy code
$ nextflow inspect -format "json" .
Pipeline is starting! 🚀
{
    "processes": [
        {
            "name": "FASTQC",
            "container": "<http://quay.io/biocontainers/fastqc:0.12.1--hdfd78af_0|quay.io/biocontainers/fastqc:0.12.1--hdfd78af_0>"
        },
        {
            "name": "TABIX_TABIX",
            "container": "<http://community.wave.seqera.io/library/htslib:1.21--ff8e28a189fbecaa|community.wave.seqera.io/library/htslib:1.21--ff8e28a189fbecaa>"
        },
        {
            "name": "ENSEMBLVEP_DOWNLOAD",
            "container": "<http://community.wave.seqera.io/library/ensembl-vep:115.2--90ec797ecb088e9a|community.wave.seqera.io/library/ensembl-vep:115.2--90ec797ecb088e9a>"
        },
        {
            "name": "GATK4_BEDTOINTERVALLIST",
            "container": "<http://community.wave.seqera.io/library/gatk4_gcnvkernel:edb12e4f0bf02cd3|community.wave.seqera.io/library/gatk4_gcnvkernel:edb12e4f0bf02cd3>"
        },
        {
            "name": "MULTIQC",
            "container": "<http://community.wave.seqera.io/library/multiqc:1.31--1efbafd542a23882|community.wave.seqera.io/library/multiqc:1.31--1efbafd542a23882>"
        },
        {
            "name": "TABIX_BGZIPTABIX",
            "container": "<http://community.wave.seqera.io/library/htslib:1.21--ff8e28a189fbecaa|community.wave.seqera.io/library/htslib:1.21--ff8e28a189fbecaa>"
        },
        {
            "name": "GTF2BED",
            "container": "<http://quay.io/biocontainers/r-base:3.5.1|quay.io/biocontainers/r-base:3.5.1>"
        },
        {
            "name": "GATK4_CREATESEQUENCEDICTIONARY",
            "container": "<http://community.wave.seqera.io/library/gatk4_gcnvkernel:edb12e4f0bf02cd3|community.wave.seqera.io/library/gatk4_gcnvkernel:edb12e4f0bf02cd3>"
        },
        {
            "name": "GATK4_APPLYBQSR",
            "container": "<http://community.wave.seqera.io/library/gatk4_gcnvkernel:edb12e4f0bf02cd3|community.wave.seqera.io/library/gatk4_gcnvkernel:edb12e4f0bf02cd3>"
        },
        {
            "name": "GATK4_BASERECALIBRATOR",
            "container": "<http://community.wave.seqera.io/library/gatk4_gcnvkernel:edb12e4f0bf02cd3|community.wave.seqera.io/library/gatk4_gcnvkernel:edb12e4f0bf02cd3>"
        },
        {
            "name": "SAMTOOLS_SORT",
            "container": "<http://quay.io/biocontainers/samtools:1.22.1--h96c455f_0|quay.io/biocontainers/samtools:1.22.1--h96c455f_0>"
        },
        {
            "name": "STAR_INDEXVERSION",
            "container": "<http://community.wave.seqera.io/library/htslib_samtools_star_gawk:ae438e9a604351a4|community.wave.seqera.io/library/htslib_samtools_star_gawk:ae438e9a604351a4>"
        },
        {
            "name": "SAMTOOLS_MERGE",
            "container": "<http://quay.io/biocontainers/samtools:1.22.1--h96c455f_0|quay.io/biocontainers/samtools:1.22.1--h96c455f_0>"
        },
        {
            "name": "GFFREAD",
            "container": "<http://quay.io/biocontainers/gffread:0.12.7--hdcf5f25_4|quay.io/biocontainers/gffread:0.12.7--hdcf5f25_4>"
        },
        {
            "name": "PICARD_MARKDUPLICATES",
            "container": "<http://community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6|community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6>"
        },
        {
            "name": "UMITOOLS_EXTRACT",
            "container": "<http://quay.io/biocontainers/umi_tools:1.1.6--py311haab0aaa_0|quay.io/biocontainers/umi_tools:1.1.6--py311haab0aaa_0>"
        },
        {
            "name": "SNPEFF_DOWNLOAD",
            "container": "<http://community.wave.seqera.io/library/snpeff:5.3.0a--ca8e0b08f227a463|community.wave.seqera.io/library/snpeff:5.3.0a--ca8e0b08f227a463>"
        },
        {
            "name": "CAT_FASTQ",
            "container": "<http://community.wave.seqera.io/library/coreutils_grep_gzip_lbzip2_pruned:838ba80435a629f8|community.wave.seqera.io/library/coreutils_grep_gzip_lbzip2_pruned:838ba80435a629f8>"
        },
        {
            "name": "GUNZIP",
            "container": "<http://community.wave.seqera.io/library/coreutils_grep_gzip_lbzip2_pruned:838ba80435a629f8|community.wave.seqera.io/library/coreutils_grep_gzip_lbzip2_pruned:838ba80435a629f8>"
        },
        {
            "name": "GATK4_MERGEVCFS",
            "container": "<http://community.wave.seqera.io/library/gatk4_gcnvkernel:edb12e4f0bf02cd3|community.wave.seqera.io/library/gatk4_gcnvkernel:edb12e4f0bf02cd3>"
        },
        {
            "name": "SAMTOOLS_FAIDX",
            "container": "<http://quay.io/biocontainers/samtools:1.22.1--h96c455f_0|quay.io/biocontainers/samtools:1.22.1--h96c455f_0>"
        },
        {
            "name": "UNTAR",
            "container": "<http://community.wave.seqera.io/library/coreutils_grep_gzip_lbzip2_pruned:838ba80435a629f8|community.wave.seqera.io/library/coreutils_grep_gzip_lbzip2_pruned:838ba80435a629f8>"
        },
        {
            "name": "GATK4_COMBINEGVCFS",
            "container": "<http://community.wave.seqera.io/library/gatk4_gcnvkernel:edb12e4f0bf02cd3|community.wave.seqera.io/library/gatk4_gcnvkernel:edb12e4f0bf02cd3>"
        },
        {
            "name": "SAMTOOLS_STATS",
            "container": "<http://quay.io/biocontainers/samtools:1.22.1--h96c455f_0|quay.io/biocontainers/samtools:1.22.1--h96c455f_0>"
        },
        {
            "name": "SAMTOOLS_FLAGSTAT",
            "container": "<http://quay.io/biocontainers/samtools:1.22.1--h96c455f_0|quay.io/biocontainers/samtools:1.22.1--h96c455f_0>"
        },
        {
            "name": "GATK4_INDEXFEATUREFILE",
            "container": "<http://community.wave.seqera.io/library/gatk4_gcnvkernel:edb12e4f0bf02cd3|community.wave.seqera.io/library/gatk4_gcnvkernel:edb12e4f0bf02cd3>"
        },
        {
            "name": "REMOVE_UNKNOWN_REGIONS",
            "container": "<http://quay.io/biocontainers/python:3.8.3|quay.io/biocontainers/python:3.8.3>"
        },
        {
            "name": "GATK4_SPLITNCIGARREADS",
            "container": "<http://community.wave.seqera.io/library/gatk4_gcnvkernel:edb12e4f0bf02cd3|community.wave.seqera.io/library/gatk4_gcnvkernel:edb12e4f0bf02cd3>"
        },
        {
            "name": "ENSEMBLVEP_VEP",
            "container": "<http://community.wave.seqera.io/library/ensembl-vep:115.2--90ec797ecb088e9a|community.wave.seqera.io/library/ensembl-vep:115.2--90ec797ecb088e9a>"
        },
        {
            "name": "GATK4_HAPLOTYPECALLER",
            "container": "<http://community.wave.seqera.io/library/gatk4_gcnvkernel:edb12e4f0bf02cd3|community.wave.seqera.io/library/gatk4_gcnvkernel:edb12e4f0bf02cd3>"
        },
        {
            "name": "BCFTOOLS_ANNOTATE",
            "container": "<http://community.wave.seqera.io/library/bcftools_htslib:0a3fa2654b52006f|community.wave.seqera.io/library/bcftools_htslib:0a3fa2654b52006f>"
        },
        {
            "name": "GATK4_VARIANTFILTRATION",
            "container": "<http://community.wave.seqera.io/library/gatk4_gcnvkernel:edb12e4f0bf02cd3|community.wave.seqera.io/library/gatk4_gcnvkernel:edb12e4f0bf02cd3>"
        },
        {
            "name": "SNPEFF_SNPEFF",
            "container": "<http://community.wave.seqera.io/library/snpeff:5.3.0a--ca8e0b08f227a463|community.wave.seqera.io/library/snpeff:5.3.0a--ca8e0b08f227a463>"
        },
        {
            "name": "SAMTOOLS_IDXSTATS",
            "container": "<http://quay.io/biocontainers/samtools:1.22.1--h96c455f_0|quay.io/biocontainers/samtools:1.22.1--h96c455f_0>"
        },
        {
            "name": "STAR_GENOMEGENERATE",
            "container": "<http://community.wave.seqera.io/library/htslib_samtools_star_gawk:ae438e9a604351a4|community.wave.seqera.io/library/htslib_samtools_star_gawk:ae438e9a604351a4>"
        },
        {
            "name": "SEQ2HLA",
            "container": "<http://community.wave.seqera.io/library/seq2hla:2.3--26344ebe67dd0e8e|community.wave.seqera.io/library/seq2hla:2.3--26344ebe67dd0e8e>"
        },
        {
            "name": "STAR_ALIGN",
            "container": "<http://community.wave.seqera.io/library/htslib_samtools_star_gawk:ae438e9a604351a4|community.wave.seqera.io/library/htslib_samtools_star_gawk:ae438e9a604351a4>"
        },
        {
            "name": "SAMTOOLS_INDEX",
            "container": "<http://quay.io/biocontainers/samtools:1.22.1--h96c455f_0|quay.io/biocontainers/samtools:1.22.1--h96c455f_0>"
        },
        {
            "name": "GATK4_INTERVALLISTTOOLS",
            "container": "<http://community.wave.seqera.io/library/gatk4_gcnvkernel:edb12e4f0bf02cd3|community.wave.seqera.io/library/gatk4_gcnvkernel:edb12e4f0bf02cd3>"
        }
    ]
}
Pipeline complete! 👋
First and last line are the offenders
m
Nice catch
Blame @Edmund and Claude
shakefist 2
claude lurk 1
ai thumbsdown 1
And me obviously
j
(I need a bot_shakefist icon 😂 )
m
ok, so I'll remove the first and last line from plugin
and try to do a release ASAP then
🙏🏻 1
thanks
Just so you know Edmund, I am not blaming you, the work on #C08TKFDUNHG is stellar and AMAZING, and definitively going the right way
🚀 1
@Júlia Mir I am working on making this a reality https://github.com/nf-core/rnavar/pull/252
💪🏻 1
For now it works on my machine 🤣
Open in Slack
PreviousNext
Powered by