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Fix naming of GFFREAD outputs leading to null.gtf #3334

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Fix naming of GFFREAD outputs leading to null.gtf

Fix naming of GFFREAD outputs leading to null.gtf #3334

Triggered via pull request March 24, 2025 15:24
@milos7250milos7250
synchronize #1526
milos7250:patch
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63 errors and 36 warnings
Run tests (tests/featurecounts_group_type.nf.test singularity NF-24.04.2)
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Run tests (tests/star_rsem.nf.test docker NF-latest-everything)
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Run tests (tests/featurecounts_group_type.nf.test docker NF-24.04.2)
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
Run tests (subworkflows/local/prepare_genome/tests/main.nf.test docker NF-24.04.2)
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
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Run tests (tests/default.nf.test docker NF-24.04.2)
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Run tests (tests/featurecounts_group_type.nf.test docker NF-latest-everything)
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Run tests (tests/kallisto.nf.test docker NF-24.04.2)
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Run tests (tests/kallisto.nf.test singularity NF-24.04.2)
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Run tests (tests/min_mapped_reads.nf.test docker NF-latest-everything)
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Run tests (tests/remove_ribo_rna.nf.test docker NF-latest-everything)
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Run tests (tests/skip_trimming.nf.test docker NF-latest-everything)
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Run tests (tests/salmon.nf.test docker NF-24.04.2)
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
Run tests (tests/salmon.nf.test singularity NF-24.04.2)
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Run tests (tests/umi.nf.test docker NF-latest-everything)
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Run tests (tests/umi.nf.test docker NF-latest-everything)
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
Run tests (tests/umi.nf.test docker NF-latest-everything)
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Run tests (tests/skip_trimming.nf.test singularity NF-24.04.2)
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
Run tests (tests/min_mapped_reads.nf.test singularity NF-24.04.2)
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
Run tests (tests/hisat2.nf.test docker NF-24.04.2)
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Run tests (tests/min_mapped_reads.nf.test docker NF-24.04.2)
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
Run tests (tests/skip_trimming.nf.test docker NF-24.04.2)
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
Run tests (tests/hisat2.nf.test docker NF-latest-everything)
Process completed with exit code 1.
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❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
Run tests (tests/hisat2.nf.test docker NF-latest-everything)
Process completed with exit code 1.
Run tests (tests/star_rsem.nf.test docker NF-24.04.2)
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
Run tests (tests/hisat2.nf.test singularity NF-24.04.2)
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
Run tests (tests/hisat2.nf.test singularity NF-24.04.2)
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Run tests (subworkflows/local/prepare_genome/tests/main.nf.test docker NF-latest-everything)
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Run tests (tests/skip_qc.nf.test docker NF-24.04.2)
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
Run tests (tests/remove_ribo_rna.nf.test singularity NF-24.04.2)
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Run tests (tests/remove_ribo_rna.nf.test docker NF-24.04.2)
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Run tests (tests/umi.nf.test singularity NF-24.04.2)
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
Run tests (tests/umi.nf.test docker NF-24.04.2)
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Run tests (tests/default.nf.test singularity NF-24.04.2)
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
Run tests (tests/skip_qc.nf.test singularity NF-24.04.2)
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
Run tests (tests/star_rsem.nf.test singularity NF-24.04.2)
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Run tests (tests/featurecounts_group_type.nf.test singularity NF-24.04.2)
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Run tests (tests/star_rsem.nf.test docker NF-latest-everything)
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Run tests (subworkflows/local/prepare_genome/tests/main.nf.test singularity NF-24.04.2)
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
Run tests (tests/featurecounts_group_type.nf.test docker NF-24.04.2)
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Run tests (subworkflows/local/prepare_genome/tests/main.nf.test docker NF-24.04.2)
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
Run tests (tests/default.nf.test docker NF-latest-everything)
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
Run tests (tests/skip_qc.nf.test docker NF-latest-everything)
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
Run tests (tests/salmon.nf.test docker NF-latest-everything)
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
Run tests (tests/default.nf.test docker NF-24.04.2)
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Run tests (tests/featurecounts_group_type.nf.test docker NF-latest-everything)
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Run tests (tests/kallisto.nf.test docker NF-24.04.2)
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Run tests (tests/kallisto.nf.test docker NF-latest-everything)
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Run tests (tests/kallisto.nf.test singularity NF-24.04.2)
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Run tests (tests/min_mapped_reads.nf.test docker NF-latest-everything)
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Run tests (tests/remove_ribo_rna.nf.test docker NF-latest-everything)
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Run tests (tests/skip_trimming.nf.test docker NF-latest-everything)
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
Run tests (tests/salmon.nf.test docker NF-24.04.2)
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Run tests (tests/salmon.nf.test singularity NF-24.04.2)
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Run tests (tests/skip_trimming.nf.test singularity NF-24.04.2)
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Run tests (tests/hisat2.nf.test docker NF-24.04.2)
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Run tests (tests/min_mapped_reads.nf.test docker NF-24.04.2)
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
Run tests (tests/skip_trimming.nf.test docker NF-24.04.2)
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
Run tests (tests/hisat2.nf.test docker NF-latest-everything)
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
Run tests (tests/star_rsem.nf.test docker NF-24.04.2)
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
Run tests (tests/hisat2.nf.test singularity NF-24.04.2)
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Run tests (subworkflows/local/prepare_genome/tests/main.nf.test docker NF-latest-everything)
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Run tests (tests/skip_qc.nf.test docker NF-24.04.2)
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⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
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Run tests (tests/default.nf.test singularity NF-24.04.2)
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⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
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⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23