Process returned exit code 1 Launched as "bash --noprofile --norc -eo pipefail /home/runner/work/_actions/Wandalen/wretry.action/v1.4.10_js_action/src/script.sh" Launched at "/home/runner/work/sarek/sarek" Attempts exhausted, made 3 attempts : Attempt #1 started at : 13:44:45 GMT+0000 (Coordinated Universal Time) Attempt #2 started at : 13:45:16 GMT+0000 (Coordinated Universal Time) Attempt #3 started at : 13:45:47 GMT+0000 (Coordinated Universal Time)

skip_all_qc docker NF latest-everything

Process returned exit code 1 Launched as "bash --noprofile --norc -eo pipefail /home/runner/work/_actions/Wandalen/wretry.action/v1.4.10_js_action/src/script.sh" Launched at "/home/runner/work/sarek/sarek" Attempts exhausted, made 3 attempts : Attempt #1 started at : 13:44:57 GMT+0000 (Coordinated Universal Time) Attempt #2 started at : 13:45:28 GMT+0000 (Coordinated Universal Time) Attempt #3 started at : 13:46:00 GMT+0000 (Coordinated Universal Time)

save_mapped_only docker NF 23.04.0

Process returned exit code 1 Launched as "bash --noprofile --norc -eo pipefail /home/runner/work/_actions/Wandalen/wretry.action/v1.4.10_js_action/src/script.sh" Launched at "/home/runner/work/sarek/sarek" Attempts exhausted, made 3 attempts : Attempt #1 started at : 13:44:55 GMT+0000 (Coordinated Universal Time) Attempt #2 started at : 13:45:27 GMT+0000 (Coordinated Universal Time) Attempt #3 started at : 13:45:59 GMT+0000 (Coordinated Universal Time)

skip_all_qc docker NF 23.04.0

Process returned exit code 1 Launched as "bash --noprofile --norc -eo pipefail /home/runner/work/_actions/Wandalen/wretry.action/v1.4.10_js_action/src/script.sh" Launched at "/home/runner/work/sarek/sarek" Attempts exhausted, made 3 attempts : Attempt #1 started at : 13:45:16 GMT+0000 (Coordinated Universal Time) Attempt #2 started at : 13:45:47 GMT+0000 (Coordinated Universal Time) Attempt #3 started at : 13:46:18 GMT+0000 (Coordinated Universal Time)

save_mapped_only docker NF latest-everything

Process returned exit code 1 Launched as "bash --noprofile --norc -eo pipefail /home/runner/work/_actions/Wandalen/wretry.action/v1.4.10_js_action/src/script.sh" Launched at "/home/runner/work/sarek/sarek" Attempts exhausted, made 3 attempts : Attempt #1 started at : 13:45:15 GMT+0000 (Coordinated Universal Time) Attempt #2 started at : 13:45:48 GMT+0000 (Coordinated Universal Time) Attempt #3 started at : 13:46:19 GMT+0000 (Coordinated Universal Time)

save_output_as_bam_only docker NF 23.04.0

Process returned exit code 1 Launched as "bash --noprofile --norc -eo pipefail /home/runner/work/_actions/Wandalen/wretry.action/v1.4.10_js_action/src/script.sh" Launched at "/home/runner/work/sarek/sarek" Attempts exhausted, made 3 attempts : Attempt #1 started at : 13:45:13 GMT+0000 (Coordinated Universal Time) Attempt #2 started at : 13:45:46 GMT+0000 (Coordinated Universal Time) Attempt #3 started at : 13:46:17 GMT+0000 (Coordinated Universal Time)

default docker NF latest-everything

Process returned exit code 1 Launched as "bash --noprofile --norc -eo pipefail /home/runner/work/_actions/Wandalen/wretry.action/v1.4.10_js_action/src/script.sh" Launched at "/home/runner/work/sarek/sarek" Attempts exhausted, made 3 attempts : Attempt #1 started at : 13:45:33 GMT+0000 (Coordinated Universal Time) Attempt #2 started at : 13:46:06 GMT+0000 (Coordinated Universal Time) Attempt #3 started at : 13:46:36 GMT+0000 (Coordinated Universal Time)

tumor_normal_pair docker NF 23.04.0

Process returned exit code 1 Launched as "bash --noprofile --norc -eo pipefail /home/runner/work/_actions/Wandalen/wretry.action/v1.4.10_js_action/src/script.sh" Launched at "/home/runner/work/sarek/sarek" Attempts exhausted, made 3 attempts : Attempt #1 started at : 13:45:44 GMT+0000 (Coordinated Universal Time) Attempt #2 started at : 13:46:16 GMT+0000 (Coordinated Universal Time) Attempt #3 started at : 13:46:46 GMT+0000 (Coordinated Universal Time)

default docker NF 23.04.0

Process returned exit code 1 Launched as "bash --noprofile --norc -eo pipefail /home/runner/work/_actions/Wandalen/wretry.action/v1.4.10_js_action/src/script.sh" Launched at "/home/runner/work/sarek/sarek" Attempts exhausted, made 3 attempts : Attempt #1 started at : 13:46:04 GMT+0000 (Coordinated Universal Time) Attempt #2 started at : 13:46:35 GMT+0000 (Coordinated Universal Time) Attempt #3 started at : 13:47:02 GMT+0000 (Coordinated Universal Time)

bwamem docker NF 23.04.0

Process returned exit code 1 Launched as "bash --noprofile --norc -eo pipefail /home/runner/work/_actions/Wandalen/wretry.action/v1.4.10_js_action/src/script.sh" Launched at "/home/runner/work/sarek/sarek" Attempts exhausted, made 3 attempts : Attempt #1 started at : 13:44:42 GMT+0000 (Coordinated Universal Time) Attempt #2 started at : 13:45:40 GMT+0000 (Coordinated Universal Time) Attempt #3 started at : 13:46:35 GMT+0000 (Coordinated Universal Time)

save_output_as_bam_only docker NF latest-everything

Process returned exit code 1 Launched as "bash --noprofile --norc -eo pipefail /home/runner/work/_actions/Wandalen/wretry.action/v1.4.10_js_action/src/script.sh" Launched at "/home/runner/work/sarek/sarek" Attempts exhausted, made 3 attempts : Attempt #1 started at : 13:46:05 GMT+0000 (Coordinated Universal Time) Attempt #2 started at : 13:46:37 GMT+0000 (Coordinated Universal Time) Attempt #3 started at : 13:47:08 GMT+0000 (Coordinated Universal Time)

bwamem2 docker NF 23.04.0

Process returned exit code 1 Launched as "bash --noprofile --norc -eo pipefail /home/runner/work/_actions/Wandalen/wretry.action/v1.4.10_js_action/src/script.sh" Launched at "/home/runner/work/sarek/sarek" Attempts exhausted, made 3 attempts : Attempt #1 started at : 13:44:47 GMT+0000 (Coordinated Universal Time) Attempt #2 started at : 13:45:47 GMT+0000 (Coordinated Universal Time) Attempt #3 started at : 13:46:46 GMT+0000 (Coordinated Universal Time)

bwamem2 docker NF latest-everything

Process returned exit code 1 Launched as "bash --noprofile --norc -eo pipefail /home/runner/work/_actions/Wandalen/wretry.action/v1.4.10_js_action/src/script.sh" Launched at "/home/runner/work/sarek/sarek" Attempts exhausted, made 3 attempts : Attempt #1 started at : 13:44:44 GMT+0000 (Coordinated Universal Time) Attempt #2 started at : 13:45:45 GMT+0000 (Coordinated Universal Time) Attempt #3 started at : 13:46:45 GMT+0000 (Coordinated Universal Time)

dragmap docker NF latest-everything

Process returned exit code 1 Launched as "bash --noprofile --norc -eo pipefail /home/runner/work/_actions/Wandalen/wretry.action/v1.4.10_js_action/src/script.sh" Launched at "/home/runner/work/sarek/sarek" Attempts exhausted, made 3 attempts : Attempt #1 started at : 13:45:06 GMT+0000 (Coordinated Universal Time) Attempt #2 started at : 13:46:07 GMT+0000 (Coordinated Universal Time) Attempt #3 started at : 13:47:06 GMT+0000 (Coordinated Universal Time)

dragmap docker NF 23.04.0

Process returned exit code 1 Launched as "bash --noprofile --norc -eo pipefail /home/runner/work/_actions/Wandalen/wretry.action/v1.4.10_js_action/src/script.sh" Launched at "/home/runner/work/sarek/sarek" Attempts exhausted, made 3 attempts : Attempt #1 started at : 13:45:49 GMT+0000 (Coordinated Universal Time) Attempt #2 started at : 13:46:51 GMT+0000 (Coordinated Universal Time) Attempt #3 started at : 13:47:50 GMT+0000 (Coordinated Universal Time)

bwamem docker NF latest-everything

Process returned exit code 1 Launched as "bash --noprofile --norc -eo pipefail /home/runner/work/_actions/Wandalen/wretry.action/v1.4.10_js_action/src/script.sh" Launched at "/home/runner/work/sarek/sarek" Attempts exhausted, made 3 attempts : Attempt #1 started at : 13:46:00 GMT+0000 (Coordinated Universal Time) Attempt #2 started at : 13:47:05 GMT+0000 (Coordinated Universal Time) Attempt #3 started at : 13:48:05 GMT+0000 (Coordinated Universal Time)

skip_markduplicates docker NF 23.04.0

Process returned exit code 1 Launched as "bash --noprofile --norc -eo pipefail /home/runner/work/_actions/Wandalen/wretry.action/v1.4.10_js_action/src/script.sh" Launched at "/home/runner/work/sarek/sarek" Attempts exhausted, made 3 attempts : Attempt #1 started at : 13:44:45 GMT+0000 (Coordinated Universal Time) Attempt #2 started at : 13:47:09 GMT+0000 (Coordinated Universal Time) Attempt #3 started at : 13:49:30 GMT+0000 (Coordinated Universal Time)

skip_markduplicates docker NF latest-everything

Process returned exit code 1 Launched as "bash --noprofile --norc -eo pipefail /home/runner/work/_actions/Wandalen/wretry.action/v1.4.10_js_action/src/script.sh" Launched at "/home/runner/work/sarek/sarek" Attempts exhausted, made 3 attempts : Attempt #1 started at : 13:45:52 GMT+0000 (Coordinated Universal Time) Attempt #2 started at : 13:48:22 GMT+0000 (Coordinated Universal Time) Attempt #3 started at : 13:50:51 GMT+0000 (Coordinated Universal Time)

confirm-pass

Process completed with exit code 1.

validation_checks docker NF latest-everything

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, nf-core/setup-nextflow@v1, actions/cache@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

validation_checks docker NF 23.04.0

pipeline_sarek docker NF 23.04.0

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-java@v3, nf-core/setup-nextflow@v1, actions/cache@v3, conda-incubator/setup-miniconda@v2. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

pipeline_sarek docker NF latest-everything

tumor_normal_pair docker NF latest-everything

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, nf-core/setup-nextflow@v1, actions/cache@v3, actions/upload-artifact@v2. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

tumor_normal_pair docker NF latest-everything

The following actions uses node12 which is deprecated and will be forced to run on node16: actions/upload-artifact@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/

skip_all_qc docker NF latest-everything