diff --git a/runs/kallisto/2024-08-05_13-50.log b/runs/kallisto/2024-08-05_13-50.log
deleted file mode 100644
index 0c3d4588dde5e52748e43bdb92ba6d322bab2851..0000000000000000000000000000000000000000
--- a/runs/kallisto/2024-08-05_13-50.log
+++ /dev/null
@@ -1,532 +0,0 @@
-[1;30mINFO[0m /home/brilator/miniconda3/bin/cwltool 3.1.20240508115724
-[1;30mINFO[0m Resolved '../../workflows/kallisto/kallisto-workflow.cwl' to 'file:///home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/workflows/kallisto/kallisto-workflow.cwl'
-[1;30mINFO[0m [workflow ] start
-[1;30mINFO[0m [workflow ] starting step index
-[1;30mINFO[0m [step index] start
-[1;30mINFO[0m [job index] Using cached output in /home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/c232c80e27f9ac9aff6ffb527ebd4189
-[1;30mINFO[0m [step index] completed success
-[1;30mINFO[0m [workflow ] starting step quant
-[1;30mINFO[0m [step quant] start
-[1;30mINFO[0m [job quant] Output of job will be cached in /home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/04c1d3666d36fb428efa31aedbcef3e7
-[1;30mINFO[0m [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
-
-[1;30mINFO[0m [job quant] Max memory used: 283MiB
-[1;30mINFO[0m [job quant] completed success
-[1;30mINFO[0m [step quant] start
-[1;30mINFO[0m [job quant_2] Output of job will be cached in /home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/ca52501ef3b3047551f9124c1d5004b4
-[1;30mINFO[0m [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
-
-[1;30mINFO[0m [job quant_2] Max memory used: 283MiB
-[1;30mINFO[0m [job quant_2] completed success
-[1;30mINFO[0m [step quant] start
-[1;30mINFO[0m [job quant_3] Output of job will be cached in /home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/c4753612931c39e236518d2ca4455d3d
-[1;30mINFO[0m [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
-
-[1;30mINFO[0m [job quant_3] Max memory used: 283MiB
-[1;30mINFO[0m [job quant_3] completed success
-[1;30mINFO[0m [step quant] start
-[1;30mINFO[0m [job quant_4] Output of job will be cached in /home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/7fa99fa2914046d103fe5e619913fef3
-[1;30mINFO[0m [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
-
-[1;30mINFO[0m [job quant_4] Max memory used: 283MiB
-[1;30mINFO[0m [job quant_4] completed success
-[1;30mINFO[0m [step quant] start
-[1;30mINFO[0m [job quant_5] Output of job will be cached in /home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/6475ad7bb21ae6103cbbd215f880611a
-[1;30mINFO[0m [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)
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[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
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[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
-
-[1;30mINFO[0m [job quant_5] Max memory used: 283MiB
-[1;30mINFO[0m [job quant_5] completed success
-[1;30mINFO[0m [step quant] start
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- --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 \
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- --cidfile=/tmp/_nyrkq_n/20240805141801-155673.cid \
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- --bootstrap-samples=30 \
- --fragment-length=200 \
- --sd \
- 20 \
- --index \
- /var/lib/cwl/stg34703b5f-6fb1-4f01-9926-b3250461e42b/Talinum.gm.CDS.nt.kallistoIndex \
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- /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
-
-[1;30mINFO[0m [job quant_6] Max memory used: 283MiB
-[1;30mINFO[0m [job quant_6] completed success
-[1;30mINFO[0m [step quant] completed success
-[1;30mINFO[0m [workflow ] starting step collectResults
-[1;30mINFO[0m [step collectResults] start
-[1;30mINFO[0m [step collectResults] start
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-[1;30mINFO[0m [step collectResults] start
-[1;30mINFO[0m [step collectResults] start
-[1;30mINFO[0m [step collectResults] completed success
-[1;30mINFO[0m [workflow ] completed success
-{
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diff --git a/runs/shiny/out/shiny_prep.RData b/runs/shiny/out/shiny_prep.RData
deleted file mode 100644
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@@ -0,0 +1,18 @@
+#!/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: []
diff --git a/runs/shiny/run.yml b/runs/shiny/run.yml
index 98c88c6cfa62eae5e623887de1d03f76f12d2095..1430c8203b6e3d91fc4283c280b3f4aaa2ad374f 100644
--- a/runs/shiny/run.yml
+++ b/runs/shiny/run.yml
@@ -1,3 +1,4 @@
in_kallisto_df:
class: File
- path: ../sleuth/out/kallisto_df.csv
\ No newline at end of file
+ path: ../../runs/sleuth/results/kallisto_df.csv
+exp_factor: "Factor..Photosynthesis.mode."
\ No newline at end of file
diff --git a/workflows/shiny/01-shiny-prep.R b/workflows/shiny/01-shiny-prep.R
deleted file mode 100644
index b8ae084aa7c21681fda025b464f5eb349187a8a5..0000000000000000000000000000000000000000
--- a/workflows/shiny/01-shiny-prep.R
+++ /dev/null
@@ -1,10 +0,0 @@
-#!/usr/bin/env Rscript
-
-args <- commandArgs(trailingOnly = T)
-in_kallisto_df <- args[1]
-
-expression_data <- read.csv(file = in_kallisto_df)
-
-available_genes <- unique(expression_data$target_id)
-
-save(expression_data, available_genes, file = "01-shiny-prep.RData")
diff --git a/workflows/shiny/01-shiny-prep.RData b/workflows/shiny/01-shiny-prep.RData
deleted file mode 100644
index 8750b371cd209ce904e08c21baac6b33a0be908a..0000000000000000000000000000000000000000
Binary files a/workflows/shiny/01-shiny-prep.RData and /dev/null differ
diff --git a/workflows/shiny/01-shiny-prep.yml b/workflows/shiny/01-shiny-prep.yml
deleted file mode 100644
index b2ec0e3b78cda23f9085bd0625f52ecaabc25345..0000000000000000000000000000000000000000
--- a/workflows/shiny/01-shiny-prep.yml
+++ /dev/null
@@ -1,3 +0,0 @@
-in_kallisto_df:
- class: File
- path: ../../runs/sleuth/results/kallisto_df.csv
\ No newline at end of file
diff --git a/workflows/shiny/02-shiny-app.R b/workflows/shiny/shiny-app.R
similarity index 84%
rename from workflows/shiny/02-shiny-app.R
rename to workflows/shiny/shiny-app.R
index e2b3c8d56094dba4ebd5625a05d3878e22fd0c52..4c020248813f9dfe57180989361fa246103f07a7 100644
--- a/workflows/shiny/02-shiny-app.R
+++ b/workflows/shiny/shiny-app.R
@@ -1,17 +1,23 @@
-
#!/usr/bin/env Rscript
-args <- commandArgs(trailingOnly = T)
-shiny_prep_data <- args[1]
-
# Load libraries
library(shiny)
library(RColorBrewer)
+library(ggplot2)
+
+# CLI arguments
+
+args <- commandArgs(trailingOnly = T)
+in_kallisto_df <- args[1]
+exp_factor <- args[2]
# Load data
-load(file = shiny_prep_data)
+expression_data <- read.csv(file = in_kallisto_df)
+available_genes <- unique(expression_data$target_id)
+
+expression_data$condition = expression_data[,exp_factor]
# Design app
diff --git a/workflows/shiny/01-shiny-prep.cwl b/workflows/shiny/workflow.cwl
similarity index 62%
rename from workflows/shiny/01-shiny-prep.cwl
rename to workflows/shiny/workflow.cwl
index c79fdeec7154c8cf0638664ad6ffd3afaad75a77..2e80423e1801af7875f5917f15ff4f704afa2c9e 100644
--- a/workflows/shiny/01-shiny-prep.cwl
+++ b/workflows/shiny/workflow.cwl
@@ -10,22 +10,22 @@ class: CommandLineTool
requirements:
- class: InitialWorkDirRequirement
listing:
- - entryname: 01-shiny-prep.R
+ - entryname: shiny-app.R
entry:
- $include: 01-shiny-prep.R
+ $include: shiny-app.R
- class: NetworkAccess
networkAccess: true
-baseCommand: [Rscript, 01-shiny-prep.R]
+baseCommand: [Rscript, shiny-app.R]
inputs:
in_kallisto_df:
type: File
inputBinding:
position: 1
+ exp_factor:
+ type: string
+ inputBinding:
+ position: 2
-outputs:
- outdir:
- type: File
- outputBinding:
- glob: "01-shiny-prep.RData"
\ No newline at end of file
+outputs: []
\ No newline at end of file