nf-core CI

Add kmcp classifier #1101

Triggered via pull request July 27, 2023 14:24

sofstam

synchronize #312

sofstam:add_kmcp_dev

Status Cancelled

Total duration 2m 45s

Artifacts –

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ci.yml

on: pull_request

Matrix: Test KrakenUniq with workflow parameters

Matrix: Test MALT with workflow parameters

Matrix: Test mOTUs with workflow parameters

Matrix: Run pipeline with test data

Annotations

16 errors and 16 warnings

Run pipeline with test data (latest-everything, --shortread_complexityfilter_tool bbduk)

Process returned exit code 1 Launched as "nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results --shortread_complexityfilter_tool bbduk" Launched at "/home/runner/work/taxprofiler/taxprofiler" Attempts exhausted, made 3 attempts : Attempt #1 started at : 14:24:49 GMT+0000 (Coordinated Universal Time) Attempt #2 started at : 14:25:07 GMT+0000 (Coordinated Universal Time) Attempt #3 started at : 14:25:23 GMT+0000 (Coordinated Universal Time)

Run pipeline with test data (23.04.0, --shortread_complexityfilter_tool bbduk)

Process returned exit code 1 Launched as "nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results --shortread_complexityfilter_tool bbduk" Launched at "/home/runner/work/taxprofiler/taxprofiler" Attempts exhausted, made 3 attempts : Attempt #1 started at : 14:24:48 GMT+0000 (Coordinated Universal Time) Attempt #2 started at : 14:25:07 GMT+0000 (Coordinated Universal Time) Attempt #3 started at : 14:25:23 GMT+0000 (Coordinated Universal Time)

Test MALT with workflow parameters (latest-everything)

Process returned exit code 1 Launched as "nextflow run ${GITHUB_WORKSPACE} -profile test_nothing,docker --run_malt --input 'https://github.com/nf-core/test-datasets/raw/taxprofiler/samplesheet_shortreadsonly.csv' --outdir ./results" Launched at "/home/runner/work/taxprofiler/taxprofiler" Attempts exhausted, made 3 attempts : Attempt #1 started at : 14:24:50 GMT+0000 (Coordinated Universal Time) Attempt #2 started at : 14:25:08 GMT+0000 (Coordinated Universal Time) Attempt #3 started at : 14:25:24 GMT+0000 (Coordinated Universal Time)

Run pipeline with test data (23.04.0, --preprocessing_qc_tool falco)

Process returned exit code 1 Launched as "nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results --preprocessing_qc_tool falco" Launched at "/home/runner/work/taxprofiler/taxprofiler" Attempts exhausted, made 3 attempts : Attempt #1 started at : 14:24:52 GMT+0000 (Coordinated Universal Time) Attempt #2 started at : 14:25:12 GMT+0000 (Coordinated Universal Time) Attempt #3 started at : 14:25:28 GMT+0000 (Coordinated Universal Time)

Run pipeline with test data (23.04.0, --shortread_qc_tool fastp)

Process returned exit code 1 Launched as "nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results --shortread_qc_tool fastp" Launched at "/home/runner/work/taxprofiler/taxprofiler" Attempts exhausted, made 3 attempts : Attempt #1 started at : 14:24:53 GMT+0000 (Coordinated Universal Time) Attempt #2 started at : 14:25:12 GMT+0000 (Coordinated Universal Time) Attempt #3 started at : 14:25:28 GMT+0000 (Coordinated Universal Time)

Run pipeline with test data (latest-everything, --shortread_qc_tool adapterremoval)

Process returned exit code 1 Launched as "nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results --shortread_qc_tool adapterremoval" Launched at "/home/runner/work/taxprofiler/taxprofiler" Attempts exhausted, made 3 attempts : Attempt #1 started at : 14:24:58 GMT+0000 (Coordinated Universal Time) Attempt #2 started at : 14:25:17 GMT+0000 (Coordinated Universal Time) Attempt #3 started at : 14:25:33 GMT+0000 (Coordinated Universal Time)

Test KrakenUniq with workflow parameters (23.04.0)

Process returned exit code 1 Launched as "nextflow run ${GITHUB_WORKSPACE} -profile test_krakenuniq,docker --outdir ./results" Launched at "/home/runner/work/taxprofiler/taxprofiler" Attempts exhausted, made 3 attempts : Attempt #1 started at : 14:24:54 GMT+0000 (Coordinated Universal Time) Attempt #2 started at : 14:25:14 GMT+0000 (Coordinated Universal Time) Attempt #3 started at : 14:25:31 GMT+0000 (Coordinated Universal Time)

Test MALT with workflow parameters (23.04.0)

The operation was canceled.

Run pipeline with test data (23.04.0, --shortread_qc_tool adapterremoval)

Process returned exit code 1 Launched as "nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results --shortread_qc_tool adapterremoval" Launched at "/home/runner/work/taxprofiler/taxprofiler" Attempts exhausted, made 3 attempts : Attempt #1 started at : 14:24:54 GMT+0000 (Coordinated Universal Time) Attempt #2 started at : 14:25:15 GMT+0000 (Coordinated Universal Time) Attempt #3 started at : 14:25:32 GMT+0000 (Coordinated Universal Time)

Test KrakenUniq with workflow parameters (latest-everything)

Process returned exit code 1 Launched as "nextflow run ${GITHUB_WORKSPACE} -profile test_krakenuniq,docker --outdir ./results" Launched at "/home/runner/work/taxprofiler/taxprofiler" Attempts exhausted, made 3 attempts : Attempt #1 started at : 14:24:54 GMT+0000 (Coordinated Universal Time) Attempt #2 started at : 14:25:16 GMT+0000 (Coordinated Universal Time) Attempt #3 started at : 14:25:32 GMT+0000 (Coordinated Universal Time)

Run pipeline with test data (23.04.0, --shortread_complexityfilter_tool prinseqplusplus)

Process returned exit code 1 Launched as "nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results --shortread_complexityfilter_tool prinseqplusplus" Launched at "/home/runner/work/taxprofiler/taxprofiler" Attempts exhausted, made 3 attempts : Attempt #1 started at : 14:24:51 GMT+0000 (Coordinated Universal Time) Attempt #2 started at : 14:25:15 GMT+0000 (Coordinated Universal Time) Attempt #3 started at : 14:25:34 GMT+0000 (Coordinated Universal Time)

Run pipeline with test data (latest-everything, --preprocessing_qc_tool falco)

Process returned exit code 1 Launched as "nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results --preprocessing_qc_tool falco" Launched at "/home/runner/work/taxprofiler/taxprofiler" Attempts exhausted, made 3 attempts : Attempt #1 started at : 14:24:58 GMT+0000 (Coordinated Universal Time) Attempt #2 started at : 14:25:20 GMT+0000 (Coordinated Universal Time) Attempt #3 started at : 14:25:40 GMT+0000 (Coordinated Universal Time)

Run pipeline with test data (latest-everything, --shortread_qc_tool fastp)

Process returned exit code 1 Launched as "nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results --shortread_qc_tool fastp" Launched at "/home/runner/work/taxprofiler/taxprofiler" Attempts exhausted, made 3 attempts : Attempt #1 started at : 14:24:56 GMT+0000 (Coordinated Universal Time) Attempt #2 started at : 14:25:17 GMT+0000 (Coordinated Universal Time) Attempt #3 started at : 14:25:35 GMT+0000 (Coordinated Universal Time)

Run pipeline with test data (latest-everything, --shortread_complexityfilter_tool prinseqplusplus)

Process returned exit code 1 Launched as "nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results --shortread_complexityfilter_tool prinseqplusplus" Launched at "/home/runner/work/taxprofiler/taxprofiler" Attempts exhausted, made 3 attempts : Attempt #1 started at : 14:24:53 GMT+0000 (Coordinated Universal Time) Attempt #2 started at : 14:25:18 GMT+0000 (Coordinated Universal Time) Attempt #3 started at : 14:25:39 GMT+0000 (Coordinated Universal Time)

Test mOTUs with workflow parameters (23.04.0)

The operation was canceled.

Test mOTUs with workflow parameters (latest-everything)

The operation was canceled.

Run pipeline with test data (latest-everything, --shortread_complexityfilter_tool bbduk)

The following actions uses node12 which is deprecated and will be forced to run on node16: Wandalen/[email protected]. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/

Run pipeline with test data (23.04.0, --shortread_complexityfilter_tool bbduk)