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Commit 57794e2f authored by Dominik Brilhaus's avatar Dominik Brilhaus
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Merge branch 'cwl-shiny' into 'main' 

Cwl shiny

See merge request !13
parents 8c03b76a 988ac506
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1 merge request!13Cwl shiny
Pipeline #9369 passed
Stage: arc_json
    Stage: quality_report_generator
      Stage: quality_report
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        with 121 additions and 725 deletions
        runs/kallisto/2024-08-05_13-50.log deleted 100644 → 0
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        View file @ 8c03b76a
        INFO /home/brilator/miniconda3/bin/cwltool 3.1.20240508115724
        INFO Resolved '../../workflows/kallisto/kallisto-workflow.cwl' to 'file:///home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/workflows/kallisto/kallisto-workflow.cwl'
        INFO [workflow ] start
        INFO [workflow ] starting step index
        INFO [step index] start
        INFO [job index] Using cached output in /home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/c232c80e27f9ac9aff6ffb527ebd4189
        INFO [step index] completed success
        INFO [workflow ] starting step quant
        INFO [step quant] start
        INFO [job quant] Output of job will be cached in /home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/04c1d3666d36fb428efa31aedbcef3e7
        INFO [job quant] /home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/04c1d3666d36fb428efa31aedbcef3e7$ docker \
        run \
        -i \
        --mount=type=bind,source=/home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/04c1d3666d36fb428efa31aedbcef3e7,target=/gvSNJe \
        --mount=type=bind,source=/tmp/mbmkyli1,target=/tmp \
        --mount=type=bind,source=/home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/c232c80e27f9ac9aff6ffb527ebd4189/Talinum.gm.CDS.nt.kallistoIndex,target=/var/lib/cwl/stg2d88a9bc-457d-4cc9-8603-fe974737cab6/Talinum.gm.CDS.nt.kallistoIndex,readonly \
        --mount=type=bind,source=/home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/assays/Talinum_RNASeq_minimal/dataset/DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz,target=/var/lib/cwl/stg9989d547-e38c-4bcd-8449-008e2e4a2d83/DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz,readonly \
        --workdir=/gvSNJe \
        --read-only=true \
        --net=none \
        --user=1007:1007 \
        --rm \
        --cidfile=/tmp/lkq3cvxw/20240805135057-308071.cid \
        --env=TMPDIR=/tmp \
        --env=HOME=/gvSNJe \
        quay.io/biocontainers/kallisto:0.50.1--h6de1650_2 \
        kallisto \
        quant \
        --output-dir \
        DB_097 \
        --bootstrap-samples=30 \
        --fragment-length=200 \
        --sd \
        20 \
        --index \
        /var/lib/cwl/stg2d88a9bc-457d-4cc9-8603-fe974737cab6/Talinum.gm.CDS.nt.kallistoIndex \
        --single \
        /var/lib/cwl/stg9989d547-e38c-4bcd-8449-008e2e4a2d83/DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz
        [quant] fragment length distribution is truncated gaussian with mean = 200, sd = 20
        [index] k-mer length: 31
        [index] number of targets: 31,434
        [index] number of k-mers: 35,149,253
        [quant] running in single-end mode
        [quant] will process file 1: /var/lib/cwl/stg9989d547-e38c-4bcd-8449-008e2e4a2d83/DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz
        [quant] finding pseudoalignments for the reads ... [progress] 1M reads processed (69.4% mapped) [progress] 2M reads processed (69.3% mapped) [progress] 3M reads processed (69.2% mapped) [progress] 4M reads processed (69.3% mapped) [progress] 5M reads processed (69.2% mapped) [progress] 6M reads processed (69.2% mapped) [progress] 7M reads processed (69.2% mapped) [progress] 8M reads processed (69.2% mapped) [progress] 9M reads processed (69.2% mapped) [progress] 10M reads processed (69.2% mapped) done
        [quant] processed 11,071,656 reads, 7,663,833 reads pseudoaligned
        [ em] quantifying the abundances ... done
        [ em] the Expectation-Maximization algorithm ran for 460 rounds
        [bstrp] running EM for the bootstrap: 1 [bstrp] running EM for the bootstrap: 2 [bstrp] running EM for the bootstrap: 3 [bstrp] running EM for the bootstrap: 4 [bstrp] running EM for the bootstrap: 5 [bstrp] running EM for the bootstrap: 6 [bstrp] running EM for the bootstrap: 7 [bstrp] running EM for the bootstrap: 8 [bstrp] running EM for the bootstrap: 9 [bstrp] running EM for the bootstrap: 10 [bstrp] running EM for the bootstrap: 11 [bstrp] running EM for the bootstrap: 12 [bstrp] running EM for the bootstrap: 13 [bstrp] running EM for the bootstrap: 14 [bstrp] running EM for the bootstrap: 15 [bstrp] running EM for the bootstrap: 16 [bstrp] running EM for the bootstrap: 17 [bstrp] running EM for the bootstrap: 18 [bstrp] running EM for the bootstrap: 19 [bstrp] running EM for the bootstrap: 20 [bstrp] running EM for the bootstrap: 21 [bstrp] running EM for the bootstrap: 22 [bstrp] running EM for the bootstrap: 23 [bstrp] running EM for the bootstrap: 24 [bstrp] running EM for the bootstrap: 25 [bstrp] running EM for the bootstrap: 26 [bstrp] running EM for the bootstrap: 27 [bstrp] running EM for the bootstrap: 28 [bstrp] running EM for the bootstrap: 29 [bstrp] running EM for the bootstrap: 30
        INFO [job quant] Max memory used: 283MiB
        INFO [job quant] completed success
        INFO [step quant] start
        INFO [job quant_2] Output of job will be cached in /home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/ca52501ef3b3047551f9124c1d5004b4
        INFO [job quant_2] /home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/ca52501ef3b3047551f9124c1d5004b4$ docker \
        run \
        -i \
        --mount=type=bind,source=/home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/ca52501ef3b3047551f9124c1d5004b4,target=/gvSNJe \
        --mount=type=bind,source=/tmp/_x8jqxqc,target=/tmp \
        --mount=type=bind,source=/home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/c232c80e27f9ac9aff6ffb527ebd4189/Talinum.gm.CDS.nt.kallistoIndex,target=/var/lib/cwl/stg19bb2e01-3f1a-4757-8b96-b3736bb62ae2/Talinum.gm.CDS.nt.kallistoIndex,readonly \
        --mount=type=bind,source=/home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/assays/Talinum_RNASeq_minimal/dataset/DB_099_CAMMD_CTTGTA_L001_R1_001.fastq.gz,target=/var/lib/cwl/stgc8c3c1dc-aa80-4b3c-8c8a-816c343091d2/DB_099_CAMMD_CTTGTA_L001_R1_001.fastq.gz,readonly \
        --workdir=/gvSNJe \
        --read-only=true \
        --net=none \
        --user=1007:1007 \
        --rm \
        --cidfile=/tmp/1q3__lzr/20240805135536-712649.cid \
        --env=TMPDIR=/tmp \
        --env=HOME=/gvSNJe \
        quay.io/biocontainers/kallisto:0.50.1--h6de1650_2 \
        kallisto \
        quant \
        --output-dir \
        DB_099 \
        --bootstrap-samples=30 \
        --fragment-length=200 \
        --sd \
        20 \
        --index \
        /var/lib/cwl/stg19bb2e01-3f1a-4757-8b96-b3736bb62ae2/Talinum.gm.CDS.nt.kallistoIndex \
        --single \
        /var/lib/cwl/stgc8c3c1dc-aa80-4b3c-8c8a-816c343091d2/DB_099_CAMMD_CTTGTA_L001_R1_001.fastq.gz
        [quant] fragment length distribution is truncated gaussian with mean = 200, sd = 20
        [index] k-mer length: 31
        [index] number of targets: 31,434
        [index] number of k-mers: 35,149,253
        [quant] running in single-end mode
        [quant] will process file 1: /var/lib/cwl/stgc8c3c1dc-aa80-4b3c-8c8a-816c343091d2/DB_099_CAMMD_CTTGTA_L001_R1_001.fastq.gz
        [quant] finding pseudoalignments for the reads ... [progress] 1M reads processed (70.3% mapped) [progress] 2M reads processed (70.3% mapped) [progress] 3M reads processed (70.2% mapped) [progress] 4M reads processed (70.2% mapped) [progress] 5M reads processed (70.2% mapped) [progress] 6M reads processed (70.2% mapped) [progress] 7M reads processed (70.2% mapped) [progress] 8M reads processed (70.2% mapped) [progress] 9M reads processed (70.3% mapped) [progress] 10M reads processed (70.2% mapped) [progress] 11M reads processed (70.2% mapped) [progress] 12M reads processed (70.3% mapped) [progress] 13M reads processed (70.2% mapped) done
        [quant] processed 14,332,278 reads, 10,066,684 reads pseudoaligned
        [ em] quantifying the abundances ... done
        [ em] the Expectation-Maximization algorithm ran for 458 rounds
        [bstrp] running EM for the bootstrap: 1 [bstrp] running EM for the bootstrap: 2 [bstrp] running EM for the bootstrap: 3 [bstrp] running EM for the bootstrap: 4 [bstrp] running EM for the bootstrap: 5 [bstrp] running EM for the bootstrap: 6 [bstrp] running EM for the bootstrap: 7 [bstrp] running EM for the bootstrap: 8 [bstrp] running EM for the bootstrap: 9 [bstrp] running EM for the bootstrap: 10 [bstrp] running EM for the bootstrap: 11 [bstrp] running EM for the bootstrap: 12 [bstrp] running EM for the bootstrap: 13 [bstrp] running EM for the bootstrap: 14 [bstrp] running EM for the bootstrap: 15 [bstrp] running EM for the bootstrap: 16 [bstrp] running EM for the bootstrap: 17 [bstrp] running EM for the bootstrap: 18 [bstrp] running EM for the bootstrap: 19 [bstrp] running EM for the bootstrap: 20 [bstrp] running EM for the bootstrap: 21 [bstrp] running EM for the bootstrap: 22 [bstrp] running EM for the bootstrap: 23 [bstrp] running EM for the bootstrap: 24 [bstrp] running EM for the bootstrap: 25 [bstrp] running EM for the bootstrap: 26 [bstrp] running EM for the bootstrap: 27 [bstrp] running EM for the bootstrap: 28 [bstrp] running EM for the bootstrap: 29 [bstrp] running EM for the bootstrap: 30
        INFO [job quant_2] Max memory used: 283MiB
        INFO [job quant_2] completed success
        INFO [step quant] start
        INFO [job quant_3] Output of job will be cached in /home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/c4753612931c39e236518d2ca4455d3d
        INFO [job quant_3] /home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/c4753612931c39e236518d2ca4455d3d$ docker \
        run \
        -i \
        --mount=type=bind,source=/home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/c4753612931c39e236518d2ca4455d3d,target=/gvSNJe \
        --mount=type=bind,source=/tmp/0idun1z_,target=/tmp \
        --mount=type=bind,source=/home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/c232c80e27f9ac9aff6ffb527ebd4189/Talinum.gm.CDS.nt.kallistoIndex,target=/var/lib/cwl/stg4688cdf5-4be9-4a10-a2da-b72109654518/Talinum.gm.CDS.nt.kallistoIndex,readonly \
        --mount=type=bind,source=/home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/assays/Talinum_RNASeq_minimal/dataset/DB_103_CAMMD_AGTCAA_L001_R1_001.fastq.gz,target=/var/lib/cwl/stg86fb44d0-f2e4-4049-b4ea-b25fb3cc52ce/DB_103_CAMMD_AGTCAA_L001_R1_001.fastq.gz,readonly \
        --workdir=/gvSNJe \
        --read-only=true \
        --net=none \
        --user=1007:1007 \
        --rm \
        --cidfile=/tmp/u2m6ez7p/20240805140121-006110.cid \
        --env=TMPDIR=/tmp \
        --env=HOME=/gvSNJe \
        quay.io/biocontainers/kallisto:0.50.1--h6de1650_2 \
        kallisto \
        quant \
        --output-dir \
        DB_103 \
        --bootstrap-samples=30 \
        --fragment-length=200 \
        --sd \
        20 \
        --index \
        /var/lib/cwl/stg4688cdf5-4be9-4a10-a2da-b72109654518/Talinum.gm.CDS.nt.kallistoIndex \
        --single \
        /var/lib/cwl/stg86fb44d0-f2e4-4049-b4ea-b25fb3cc52ce/DB_103_CAMMD_AGTCAA_L001_R1_001.fastq.gz
        [quant] fragment length distribution is truncated gaussian with mean = 200, sd = 20
        [index] k-mer length: 31
        [index] number of targets: 31,434
        [index] number of k-mers: 35,149,253
        [quant] running in single-end mode
        [quant] will process file 1: /var/lib/cwl/stg86fb44d0-f2e4-4049-b4ea-b25fb3cc52ce/DB_103_CAMMD_AGTCAA_L001_R1_001.fastq.gz
        [quant] finding pseudoalignments for the reads ... [progress] 1M reads processed (69.0% mapped) [progress] 2M reads processed (68.9% mapped) [progress] 3M reads processed (68.9% mapped) [progress] 4M reads processed (68.9% mapped) [progress] 5M reads processed (68.9% mapped) [progress] 6M reads processed (68.9% mapped) [progress] 7M reads processed (68.9% mapped) [progress] 8M reads processed (68.9% mapped) [progress] 9M reads processed (68.9% mapped) [progress] 10M reads processed (68.9% mapped) [progress] 11M reads processed (68.9% mapped) [progress] 12M reads processed (68.9% mapped) done
        [quant] processed 13,083,957 reads, 9,007,909 reads pseudoaligned
        [ em] quantifying the abundances ... done
        [ em] the Expectation-Maximization algorithm ran for 806 rounds
        [bstrp] running EM for the bootstrap: 1 [bstrp] running EM for the bootstrap: 2 [bstrp] running EM for the bootstrap: 3 [bstrp] running EM for the bootstrap: 4 [bstrp] running EM for the bootstrap: 5 [bstrp] running EM for the bootstrap: 6 [bstrp] running EM for the bootstrap: 7 [bstrp] running EM for the bootstrap: 8 [bstrp] running EM for the bootstrap: 9 [bstrp] running EM for the bootstrap: 10 [bstrp] running EM for the bootstrap: 11 [bstrp] running EM for the bootstrap: 12 [bstrp] running EM for the bootstrap: 13 [bstrp] running EM for the bootstrap: 14 [bstrp] running EM for the bootstrap: 15 [bstrp] running EM for the bootstrap: 16 [bstrp] running EM for the bootstrap: 17 [bstrp] running EM for the bootstrap: 18 [bstrp] running EM for the bootstrap: 19 [bstrp] running EM for the bootstrap: 20 [bstrp] running EM for the bootstrap: 21 [bstrp] running EM for the bootstrap: 22 [bstrp] running EM for the bootstrap: 23 [bstrp] running EM for the bootstrap: 24 [bstrp] running EM for the bootstrap: 25 [bstrp] running EM for the bootstrap: 26 [bstrp] running EM for the bootstrap: 27 [bstrp] running EM for the bootstrap: 28 [bstrp] running EM for the bootstrap: 29 [bstrp] running EM for the bootstrap: 30
        INFO [job quant_3] Max memory used: 283MiB
        INFO [job quant_3] completed success
        INFO [step quant] start
        INFO [job quant_4] Output of job will be cached in /home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/7fa99fa2914046d103fe5e619913fef3
        INFO [job quant_4] /home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/7fa99fa2914046d103fe5e619913fef3$ docker \
        run \
        -i \
        --mount=type=bind,source=/home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/7fa99fa2914046d103fe5e619913fef3,target=/gvSNJe \
        --mount=type=bind,source=/tmp/qdidmi0d,target=/tmp \
        --mount=type=bind,source=/home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/c232c80e27f9ac9aff6ffb527ebd4189/Talinum.gm.CDS.nt.kallistoIndex,target=/var/lib/cwl/stgd1efd19f-8170-422d-b114-5ea798ac0aec/Talinum.gm.CDS.nt.kallistoIndex,readonly \
        --mount=type=bind,source=/home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/assays/Talinum_RNASeq_minimal/dataset/DB_161_reC3MD_GTCCGC_L001_R1_001.fastq.gz,target=/var/lib/cwl/stgf263d766-1fa7-41f0-8d5b-d9940c486e06/DB_161_reC3MD_GTCCGC_L001_R1_001.fastq.gz,readonly \
        --workdir=/gvSNJe \
        --read-only=true \
        --net=none \
        --user=1007:1007 \
        --rm \
        --cidfile=/tmp/fx0nz7uo/20240805140646-758938.cid \
        --env=TMPDIR=/tmp \
        --env=HOME=/gvSNJe \
        quay.io/biocontainers/kallisto:0.50.1--h6de1650_2 \
        kallisto \
        quant \
        --output-dir \
        DB_161 \
        --bootstrap-samples=30 \
        --fragment-length=200 \
        --sd \
        20 \
        --index \
        /var/lib/cwl/stgd1efd19f-8170-422d-b114-5ea798ac0aec/Talinum.gm.CDS.nt.kallistoIndex \
        --single \
        /var/lib/cwl/stgf263d766-1fa7-41f0-8d5b-d9940c486e06/DB_161_reC3MD_GTCCGC_L001_R1_001.fastq.gz
        [quant] fragment length distribution is truncated gaussian with mean = 200, sd = 20
        [index] k-mer length: 31
        [index] number of targets: 31,434
        [index] number of k-mers: 35,149,253
        [quant] running in single-end mode
        [quant] will process file 1: /var/lib/cwl/stgf263d766-1fa7-41f0-8d5b-d9940c486e06/DB_161_reC3MD_GTCCGC_L001_R1_001.fastq.gz
        [quant] finding pseudoalignments for the reads ... [progress] 1M reads processed (71.0% mapped) [progress] 2M reads processed (70.9% mapped) [progress] 3M reads processed (70.9% mapped) [progress] 4M reads processed (70.9% mapped) [progress] 5M reads processed (70.9% mapped) [progress] 6M reads processed (70.8% mapped) [progress] 7M reads processed (70.9% mapped) [progress] 8M reads processed (70.9% mapped) [progress] 9M reads processed (70.9% mapped) [progress] 10M reads processed (70.9% mapped) [progress] 11M reads processed (70.9% mapped) [progress] 12M reads processed (70.9% mapped) done
        [quant] processed 12,785,081 reads, 9,058,463 reads pseudoaligned
        [ em] quantifying the abundances ... done
        [ em] the Expectation-Maximization algorithm ran for 500 rounds
        [bstrp] running EM for the bootstrap: 1 [bstrp] running EM for the bootstrap: 2 [bstrp] running EM for the bootstrap: 3 [bstrp] running EM for the bootstrap: 4 [bstrp] running EM for the bootstrap: 5 [bstrp] running EM for the bootstrap: 6 [bstrp] running EM for the bootstrap: 7 [bstrp] running EM for the bootstrap: 8 [bstrp] running EM for the bootstrap: 9 [bstrp] running EM for the bootstrap: 10 [bstrp] running EM for the bootstrap: 11 [bstrp] running EM for the bootstrap: 12 [bstrp] running EM for the bootstrap: 13 [bstrp] running EM for the bootstrap: 14 [bstrp] running EM for the bootstrap: 15 [bstrp] running EM for the bootstrap: 16 [bstrp] running EM for the bootstrap: 17 [bstrp] running EM for the bootstrap: 18 [bstrp] running EM for the bootstrap: 19 [bstrp] running EM for the bootstrap: 20 [bstrp] running EM for the bootstrap: 21 [bstrp] running EM for the bootstrap: 22 [bstrp] running EM for the bootstrap: 23 [bstrp] running EM for the bootstrap: 24 [bstrp] running EM for the bootstrap: 25 [bstrp] running EM for the bootstrap: 26 [bstrp] running EM for the bootstrap: 27 [bstrp] running EM for the bootstrap: 28 [bstrp] running EM for the bootstrap: 29 [bstrp] running EM for the bootstrap: 30
        INFO [job quant_4] Max memory used: 283MiB
        INFO [job quant_4] completed success
        INFO [step quant] start
        INFO [job quant_5] Output of job will be cached in /home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/6475ad7bb21ae6103cbbd215f880611a
        INFO [job quant_5] /home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/6475ad7bb21ae6103cbbd215f880611a$ docker \
        run \
        -i \
        --mount=type=bind,source=/home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/6475ad7bb21ae6103cbbd215f880611a,target=/gvSNJe \
        --mount=type=bind,source=/tmp/lwmiuppe,target=/tmp \
        --mount=type=bind,source=/home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/c232c80e27f9ac9aff6ffb527ebd4189/Talinum.gm.CDS.nt.kallistoIndex,target=/var/lib/cwl/stg53b39f3b-5476-4170-8c9a-57684344461d/Talinum.gm.CDS.nt.kallistoIndex,readonly \
        --mount=type=bind,source=/home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/assays/Talinum_RNASeq_minimal/dataset/DB_163_reC3MD_GTGAAA_L001_R1_001.fastq.gz,target=/var/lib/cwl/stgba54becd-ad88-446e-971e-7b50ec97640e/DB_163_reC3MD_GTGAAA_L001_R1_001.fastq.gz,readonly \
        --workdir=/gvSNJe \
        --read-only=true \
        --net=none \
        --user=1007:1007 \
        --rm \
        --cidfile=/tmp/jf9xn6l5/20240805141155-698481.cid \
        --env=TMPDIR=/tmp \
        --env=HOME=/gvSNJe \
        quay.io/biocontainers/kallisto:0.50.1--h6de1650_2 \
        kallisto \
        quant \
        --output-dir \
        DB_163 \
        --bootstrap-samples=30 \
        --fragment-length=200 \
        --sd \
        20 \
        --index \
        /var/lib/cwl/stg53b39f3b-5476-4170-8c9a-57684344461d/Talinum.gm.CDS.nt.kallistoIndex \
        --single \
        /var/lib/cwl/stgba54becd-ad88-446e-971e-7b50ec97640e/DB_163_reC3MD_GTGAAA_L001_R1_001.fastq.gz
        [quant] fragment length distribution is truncated gaussian with mean = 200, sd = 20
        [index] k-mer length: 31
        [index] number of targets: 31,434
        [index] number of k-mers: 35,149,253
        [quant] running in single-end mode
        [quant] will process file 1: /var/lib/cwl/stgba54becd-ad88-446e-971e-7b50ec97640e/DB_163_reC3MD_GTGAAA_L001_R1_001.fastq.gz
        [quant] finding pseudoalignments for the reads ... [progress] 1M reads processed (70.4% mapped) [progress] 2M reads processed (70.3% mapped) [progress] 3M reads processed (70.3% mapped) [progress] 4M reads processed (70.3% mapped) [progress] 5M reads processed (70.3% mapped) [progress] 6M reads processed (70.3% mapped) [progress] 7M reads processed (70.2% mapped) [progress] 8M reads processed (70.3% mapped) [progress] 9M reads processed (70.3% mapped) [progress] 10M reads processed (70.3% mapped) [progress] 11M reads processed (70.3% mapped) [progress] 12M reads processed (70.3% mapped) [progress] 13M reads processed (70.3% mapped) done
        [quant] processed 14,312,514 reads, 10,054,587 reads pseudoaligned
        [ em] quantifying the abundances ... done
        [ em] the Expectation-Maximization algorithm ran for 583 rounds
        [bstrp] running EM for the bootstrap: 1 [bstrp] running EM for the bootstrap: 2 [bstrp] running EM for the bootstrap: 3 [bstrp] running EM for the bootstrap: 4 [bstrp] running EM for the bootstrap: 5 [bstrp] running EM for the bootstrap: 6 [bstrp] running EM for the bootstrap: 7 [bstrp] running EM for the bootstrap: 8 [bstrp] running EM for the bootstrap: 9 [bstrp] running EM for the bootstrap: 10 [bstrp] running EM for the bootstrap: 11 [bstrp] running EM for the bootstrap: 12 [bstrp] running EM for the bootstrap: 13 [bstrp] running EM for the bootstrap: 14 [bstrp] running EM for the bootstrap: 15 [bstrp] running EM for the bootstrap: 16 [bstrp] running EM for the bootstrap: 17 [bstrp] running EM for the bootstrap: 18 [bstrp] running EM for the bootstrap: 19 [bstrp] running EM for the bootstrap: 20 [bstrp] running EM for the bootstrap: 21 [bstrp] running EM for the bootstrap: 22 [bstrp] running EM for the bootstrap: 23 [bstrp] running EM for the bootstrap: 24 [bstrp] running EM for the bootstrap: 25 [bstrp] running EM for the bootstrap: 26 [bstrp] running EM for the bootstrap: 27 [bstrp] running EM for the bootstrap: 28 [bstrp] running EM for the bootstrap: 29 [bstrp] running EM for the bootstrap: 30
        INFO [job quant_5] Max memory used: 283MiB
        INFO [job quant_5] completed success
        INFO [step quant] start
        INFO [job quant_6] Output of job will be cached in /home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/64cab5af8057447efd20f0d6b5bc5235
        INFO [job quant_6] /home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/64cab5af8057447efd20f0d6b5bc5235$ docker \
        run \
        -i \
        --mount=type=bind,source=/home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/64cab5af8057447efd20f0d6b5bc5235,target=/gvSNJe \
        --mount=type=bind,source=/tmp/n2t1f_d1,target=/tmp \
        --mount=type=bind,source=/home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/c232c80e27f9ac9aff6ffb527ebd4189/Talinum.gm.CDS.nt.kallistoIndex,target=/var/lib/cwl/stg34703b5f-6fb1-4f01-9926-b3250461e42b/Talinum.gm.CDS.nt.kallistoIndex,readonly \
        --mount=type=bind,source=/home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/assays/Talinum_RNASeq_minimal/dataset/DB_165_re-C3MD_GTGAAA_L002_R1_001.fastq.gz,target=/var/lib/cwl/stg48c813d5-839d-404e-84c6-ba7a313e084f/DB_165_re-C3MD_GTGAAA_L002_R1_001.fastq.gz,readonly \
        --workdir=/gvSNJe \
        --read-only=true \
        --net=none \
        --user=1007:1007 \
        --rm \
        --cidfile=/tmp/_nyrkq_n/20240805141801-155673.cid \
        --env=TMPDIR=/tmp \
        --env=HOME=/gvSNJe \
        quay.io/biocontainers/kallisto:0.50.1--h6de1650_2 \
        kallisto \
        quant \
        --output-dir \
        DB_165 \
        --bootstrap-samples=30 \
        --fragment-length=200 \
        --sd \
        20 \
        --index \
        /var/lib/cwl/stg34703b5f-6fb1-4f01-9926-b3250461e42b/Talinum.gm.CDS.nt.kallistoIndex \
        --single \
        /var/lib/cwl/stg48c813d5-839d-404e-84c6-ba7a313e084f/DB_165_re-C3MD_GTGAAA_L002_R1_001.fastq.gz
        [quant] fragment length distribution is truncated gaussian with mean = 200, sd = 20
        [index] k-mer length: 31
        [index] number of targets: 31,434
        [index] number of k-mers: 35,149,253
        [quant] running in single-end mode
        [quant] will process file 1: /var/lib/cwl/stg48c813d5-839d-404e-84c6-ba7a313e084f/DB_165_re-C3MD_GTGAAA_L002_R1_001.fastq.gz
        [quant] finding pseudoalignments for the reads ... [progress] 1M reads processed (70.0% mapped) [progress] 2M reads processed (69.8% mapped) [progress] 3M reads processed (69.8% mapped) [progress] 4M reads processed (69.8% mapped) [progress] 5M reads processed (69.8% mapped) [progress] 6M reads processed (69.8% mapped) [progress] 7M reads processed (69.8% mapped) [progress] 8M reads processed (69.8% mapped) [progress] 9M reads processed (69.8% mapped) [progress] 10M reads processed (69.8% mapped) [progress] 11M reads processed (69.8% mapped) [progress] 12M reads processed (69.8% mapped) [progress] 13M reads processed (69.8% mapped) done
        [quant] processed 13,679,479 reads, 9,552,610 reads pseudoaligned
        [ em] quantifying the abundances ... done
        [ em] the Expectation-Maximization algorithm ran for 514 rounds
        [bstrp] running EM for the bootstrap: 1 [bstrp] running EM for the bootstrap: 2 [bstrp] running EM for the bootstrap: 3 [bstrp] running EM for the bootstrap: 4 [bstrp] running EM for the bootstrap: 5 [bstrp] running EM for the bootstrap: 6 [bstrp] running EM for the bootstrap: 7 [bstrp] running EM for the bootstrap: 8 [bstrp] running EM for the bootstrap: 9 [bstrp] running EM for the bootstrap: 10 [bstrp] running EM for the bootstrap: 11 [bstrp] running EM for the bootstrap: 12 [bstrp] running EM for the bootstrap: 13 [bstrp] running EM for the bootstrap: 14 [bstrp] running EM for the bootstrap: 15 [bstrp] running EM for the bootstrap: 16 [bstrp] running EM for the bootstrap: 17 [bstrp] running EM for the bootstrap: 18 [bstrp] running EM for the bootstrap: 19 [bstrp] running EM for the bootstrap: 20 [bstrp] running EM for the bootstrap: 21 [bstrp] running EM for the bootstrap: 22 [bstrp] running EM for the bootstrap: 23 [bstrp] running EM for the bootstrap: 24 [bstrp] running EM for the bootstrap: 25 [bstrp] running EM for the bootstrap: 26 [bstrp] running EM for the bootstrap: 27 [bstrp] running EM for the bootstrap: 28 [bstrp] running EM for the bootstrap: 29 [bstrp] running EM for the bootstrap: 30
        INFO [job quant_6] Max memory used: 283MiB
        INFO [job quant_6] completed success
        INFO [step quant] completed success
        INFO [workflow ] starting step collectResults
        INFO [step collectResults] start
        INFO [step collectResults] start
        INFO [step collectResults] start
        INFO [step collectResults] start
        INFO [step collectResults] start
        INFO [step collectResults] start
        INFO [step collectResults] completed success
        INFO [workflow ] completed success
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        "path": "/home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/kallisto_results"
        }
        ]
        }INFO Final process status is success
        runs/kallisto/single-steps/README.md deleted 100644 → 0
        + 0
        − 16
        View file @ 8c03b76a
        # Kallisto
        ## Executing individual steps
        ### Create genome index
        ```bash
        cwltool ../../../workflows/kallisto/kallisto-index.cwl index.yml
        ```
        ### Quantification of a single sample
        ```bash
        cwltool ../../../workflows/kallisto/kallisto-quant.cwl quant.yml
        ```
        runs/kallisto/single-steps/index.yml deleted 100644 → 0
        + 0
        − 8
        View file @ 8c03b76a
        InputFiles:
        - class: File
        path: ../../../studies/TalinumGenomeDraft/resources/Talinum.gm.CDS.nt.fa
        format: edam:format_1929 # FASTA
        IndexName: "Talinum.gm.CDS"
        $namespaces:
        edam: https://edamontology.org/
        \ No newline at end of file
        runs/kallisto/single-steps/quant.yml deleted 100644 → 0
        + 0
        − 15
        View file @ 8c03b76a
        InputReads:
        - class: File
        path: ../../../assays/Talinum_RNASeq_minimal/dataset/DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz
        format: edam:format_1930 # FASTA
        QuantOutfolder: DB_097
        Index:
        class: File
        path: ./Talinum.gm.CDS.kallistoIndex
        isSingle: true
        FragmentLength: 200
        StandardDeviation: 20
        BootstrapSamples: 30
        $namespaces:
        edam: https://edamontology.org/
        \ No newline at end of file
        runs/shiny/run.cwl 0 → 100644
        + 18
        − 0
        View file @ 57794e2f
        #!/usr/bin/env cwl-runner
        cwlVersion: v1.2
        class: Workflow
        inputs:
        in_kallisto_df: File
        exp_factor: string
        steps:
        run_shiny:
        run: ../../workflows/shiny/workflow.cwl
        in:
        in_kallisto_df: in_kallisto_df
        exp_factor: exp_factor
        out: []
        outputs: []
        runs/shiny/run.yml 0 → 100644
        + 4
        − 0
        View file @ 57794e2f
        in_kallisto_df:
        class: File
        path: ../../runs/sleuth/results/kallisto_df.csv
        exp_factor: "Factor..Photosynthesis.mode."
        \ No newline at end of file
        runs/shiny_plots.Rmd deleted 100644 → 0
        + 0
        − 77
        View file @ 8c03b76a
        ---
        title: "Plot Talinum RNASeq data"
        output: html_document
        runtime: shiny
        ---
        ```{r setup, include=FALSE}
        knitr::opts_chunk$set(echo = TRUE)
        ```
        ```{r load_data, include=FALSE}
        load(file = "../runs/shiny_prep/out/shiny_prep.RData")
        ```
        ```{r load_libraries, message=TRUE, warning=TRUE, include=FALSE}
        # Load libraries
        library(kableExtra)
        library(shiny)
        library(RColorBrewer)
        library(tidyverse)
        ```
        ```{r, eval = FALSE, echo = FALSE}
        # Non-interactive test
        current_selection <- sample(expression_data$target_id, 10)
        plot_set <- subset(expression_data, target_id %in% current_selection)
        ggplot(plot_set, aes(x = condition, y = tpm, group = condition)) +
        stat_summary(fun = "mean", geom = "bar") +
        geom_point(size = 0.5) +
        facet_wrap(~target_id, scales = "free") +
        theme_minimal()
        ```
        ```{r shiny_part, echo=FALSE, message = F, error = FALSE, warning=FALSE}
        # Let it shine
        sidebarLayout(
        sidebarPanel(
        selectizeInput(
        multiple = T, "target", label = "Select Gene by target id",
        choices = available_genes,
        selected = sample(available_genes, size = 3),
        options = list(
        delimiter = " ",
        create = I("function(input, callback){return {value: input, text: input};}")
        )
        )
        ),
        mainPanel(
        renderPlot({
        plot_set <- subset(expression_data, target_id %in% input$target)
        ## Facetted by gene only
        ggplot(plot_set, aes(x = condition, y = tpm)) +
        stat_summary(fun = "mean", geom = "bar") +
        geom_point(size = 0.5) +
        facet_wrap(~target_id, scales = "free") +
        theme_minimal() +
        theme(aspect.ratio = 1)
        }),
        )
        )
        ```
        runs/shiny_prep/out/shiny_prep.RData deleted 100644 → 0
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        runs/shiny_prep/run.cwl deleted 100644 → 0
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        #!/usr/bin/env cwl-runner
        cwlVersion: v1.2
        class: CommandLineTool
        inputs:
        - id: r_script
        type: File
        inputBinding:
        position: 0
        - id: out_folder
        type: string
        inputBinding:
        position: 1
        - id: in_kallisto_df
        type: File
        inputBinding:
        position: 2
        outputs:
        - id: outdir
        type:
        type: array
        items: Directory
        outputBinding:
        glob: $(runtime.outdir)/$(inputs.out_folder)
        baseCommand:
        - Rscript
        runs/shiny_prep/run.yml deleted 100644 → 0
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        − 8
        View file @ 8c03b76a
        cores: 1
        r_script:
        class: File
        path: ../../workflows/shiny_prep/shiny_prep.R
        in_kallisto_df:
        class: File
        path: ../sleuth/out/kallisto_df.csv
        out_folder: out
        \ No newline at end of file
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        − 0
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        − 14
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        #!/usr/bin/env cwl-runner
        cwlVersion: v1.2
        class: CommandLineTool
        requirements:
        - class: DockerRequirement
        dockerPull: quay.io/biocontainers/mulled-v2-05fd88b9ac812a9149da2f2d881d62f01cc49835:a10f0e3a7a70fc45494f8781d33901086d2214d0-0
        baseCommand: [Rscript, --help]
        inputs: []
        outputs: []
        workflows/shiny/shiny-app.R 0 → 100644
        + 68
        − 0
        View file @ 57794e2f
        #!/usr/bin/env Rscript
        # Load libraries
        library(shiny)
        library(RColorBrewer)
        library(ggplot2)
        # CLI arguments
        args <- commandArgs(trailingOnly = T)
        in_kallisto_df <- args[1]
        exp_factor <- args[2]
        # Load data
        expression_data <- read.csv(file = in_kallisto_df)
        available_genes <- unique(expression_data$target_id)
        expression_data$condition = expression_data[,exp_factor]
        # Design app
        ui <- fluidPage(
        sidebarLayout(
        sidebarPanel(
        selectizeInput(
        multiple = TRUE, "target", label = "Select Gene by target id",
        selected = sample(available_genes, size = 3),
        choices = NULL, # Start with no choices
        options = list(
        server = TRUE, # Enable server-side processing
        delimiter = " ",
        create = I("function(input, callback){return {value: input, text: input};}")
        )
        )
        ),
        mainPanel(
        plotOutput("exPlot")
        )
        )
        )
        # Server logic
        server <- function(input, output, session) {
        # Dynamically load the available genes
        observe({
        updateSelectizeInput(session, "target", choices = available_genes, server = TRUE)
        })
        output$exPlot <- renderPlot({
        plot_set <- subset(expression_data, target_id %in% input$target)
        # Facetted plot by gene
        ggplot(plot_set, aes(x = condition, y = tpm)) +
        stat_summary(fun = "mean", geom = "bar") +
        geom_point(size = 0.5) +
        facet_wrap(~target_id, scales = "free") +
        theme_minimal() +
        theme(aspect.ratio = 1)
        })
        }
        # Launch app
        shinyApp(ui, server)
        workflows/shiny/workflow.cwl 0 → 100644
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        − 0
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        #!/usr/bin/env cwl-runner
        cwlVersion: v1.2
        class: CommandLineTool
        # hints:
        # DockerRequirement:
        # dockerPull:
        requirements:
        - class: InitialWorkDirRequirement
        listing:
        - entryname: shiny-app.R
        entry:
        $include: shiny-app.R
        - class: NetworkAccess
        networkAccess: true
        baseCommand: [Rscript, shiny-app.R]
        inputs:
        in_kallisto_df:
        type: File
        inputBinding:
        position: 1
        exp_factor:
        type: string
        inputBinding:
        position: 2
        outputs: []
        \ No newline at end of file
        workflows/shiny_prep/shiny_prep.R deleted 100644 → 0
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        View file @ 8c03b76a
        #!/usr/bin/env Rscript
        ################################################
        #### Read arguments from CLI
        ################################################
        args <- commandArgs(trailingOnly = T)
        out_folder <- args[1]
        in_kallisto_df <- args[2]
        ################################################
        #### If it does not exist, create out dir
        ################################################
        dir.create(out_folder, recursive = T, showWarnings = F)
        ################################################
        #### Prep data for shiny app
        ################################################
        expression_data <- read.csv(file = in_kallisto_df)
        available_genes <- unique(expression_data$target_id)
        save(expression_data, available_genes, file = paste(out_folder, 'shiny_prep.RData', sep = "/"))
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