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stage and prod profiles #50

Merged
merged 1 commit into from
Oct 26, 2023
Merged

stage and prod profiles #50

merged 1 commit into from
Oct 26, 2023

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henningonsbring
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Background

Profiles for stage and production

Problem/Issue

What have I done

Check list

I have:

  • Tested with Stub run
  • Tested on our HPC

Sorry, something went wrong.

@henningonsbring
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Ran:
/projects/fs1/shared/external-tools/nextflow/latest/nextflow run /projects/fs1/shared/Development_Github/singleCellWorkflows -bg -profile standard,stage --samplesheet /projects/fs1/stage_shared/Jobs/2023_180/2023_180_SampleSheet.csv > /projects/fs1/stage_shared/Logs/Singlecell/2023_180_started231026_090909.log

The command finished without errors, got e-mail, see log:

cat /projects/fs1/stage_shared/Logs/Singlecell/2023_180_started231026_090909.log
N E X T F L O W  ~  version 22.04.5
Launching `/projects/fs1/shared/Development_Github/singleCellWorkflows/main.nf` [lethal_brattain] DSL2 - revision: 3890d63c78
[b0/e87c3c] Submitted process > FLEX_SCRNASEQ:SPLITSHEET
[ad/41d892] Submitted process > VISIUM:SPLITSHEET
[fe/74f1ce] Submitted process > SCMULTI:SPLITSHEET
[26/a1dd5a] Submitted process > GET_ANALYSISES
[4b/40ae03] Submitted process > SC_ATAC:SPLITSHEET
[74/4a7dac] Submitted process > SC_ARC:SPLITSHEET
[90/8a4c8e] Submitted process > SCCITESEQ:SPLITSHEET
[d5/b6d87d] Submitted process > SCRNASEQ:SPLITSHEET
[a6/dd0494] Submitted process > SCRNASEQ:FASTQC (INVR_P1B_D3)
[e2/ba7e26] Submitted process > SCRNASEQ:COUNT (INVR_P1B_D3)
[a8/f1642b] Submitted process > SCRNASEQ:FINISH_PROJECTS:MULTIQC (2023_180)
[b7/3de004] Submitted process > SCRNASEQ:FINISH_PROJECTS:SYNC_MULTIQC (2023_180)
[ec/1c9489] Submitted process > SCRNASEQ:FINISH_PROJECTS:PUBLISH_MANIFEST (2023_180)
[bf/3e0883] Submitted process > SCRNASEQ:FINISH_PROJECTS:MD5SUM (2023_180)
[6b/fdf6cf] Submitted process > SCRNASEQ:FINISH_PROJECTS:DELIVER_PROJ (2023_180)

No files was printed to prod:

ls /projects/fs1/shared/Jobs/
2022_069  2023_098  2023_114  2023_140  2023_150  2023_162    2023_184  2023_196  2023_201  2023_206_fastq  2023_214  2023_223  2023_232  bjhall     Logs
2022_179  2023_108  2023_129  2023_142  2023_159  2023_171    2023_188  2023_198  2023_203  2023_209        2023_217  2023_227  2023_237  GMS_AL
2022_206  2023_110  2023_134  2023_144  2023_160  2023_180_o  2023_190  2023_200  2023_205  2023_212        2023_219  2023_231  2023_239  HMM3HDMXY

@henningonsbring henningonsbring merged commit aae0655 into master Oct 26, 2023
@henningonsbring henningonsbring deleted the stage branch October 26, 2023 07:37
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