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)
[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
-
-[1;30mINFO[0m [job quant_5] Max memory used: 283MiB
-[1;30mINFO[0m [job quant_5] completed success
-[1;30mINFO[0m [step quant] start
-[1;30mINFO[0m [job quant_6] Output of job will be cached in /home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/64cab5af8057447efd20f0d6b5bc5235
-[1;30mINFO[0m [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
-
-[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
-[1;30mINFO[0m [step collectResults] start
-[1;30mINFO[0m [step collectResults] start
-[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
-{
- "finalOut": [
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- "listing": [
- {
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- },
- {
- "class": "File",
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- "location": "file:///home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/kallisto_results",
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- "listing": [
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- "basename": "DB_165",
- "class": "Directory",
- "listing": [
- {
- "class": "File",
- "location": "file:///home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/kallisto_results/DB_165/abundance.tsv",
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- "basename": "run_info.json",
- "size": 561,
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- },
- {
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- "location": "file:///home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/kallisto_results",
- "path": "/home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/kallisto_results"
- }
- ]
-}[1;30mINFO[0m Final process status is success
diff --git a/runs/kallisto/single-steps/README.md b/runs/kallisto/single-steps/README.md
deleted file mode 100644
index 847851e63bfed94c1b453c7c21608ce539eebdd3..0000000000000000000000000000000000000000
--- a/runs/kallisto/single-steps/README.md
+++ /dev/null
@@ -1,16 +0,0 @@
-# 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
-```
diff --git a/runs/kallisto/single-steps/index.yml b/runs/kallisto/single-steps/index.yml
deleted file mode 100644
index 70501a10d6fefd88bc7de360aafda461a41b13d7..0000000000000000000000000000000000000000
--- a/runs/kallisto/single-steps/index.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-InputFiles:
- - class: File
- path: ../../../studies/TalinumGenomeDraft/resources/Talinum.gm.CDS.nt.fa
- format: edam:format_1929 # FASTA
-IndexName: "Talinum.gm.CDS"
-
-$namespaces:
- edam: https://edamontology.org/
\ No newline at end of file
diff --git a/runs/kallisto/single-steps/quant.yml b/runs/kallisto/single-steps/quant.yml
deleted file mode 100644
index bd6cb6a8d6d73cde89d8d21e2b58b8ed37051c10..0000000000000000000000000000000000000000
--- a/runs/kallisto/single-steps/quant.yml
+++ /dev/null
@@ -1,15 +0,0 @@
-InputReads:
- - class: File
- path: ../../../assays/Talinum_RNASeq_minimal/dataset/DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz
- format: edam:format_1930 # FASTA
-QuantOutfolder: DB_097
-Index:
- class: File
- path: ./Talinum.gm.CDS.kallistoIndex
-isSingle: true
-FragmentLength: 200
-StandardDeviation: 20
-BootstrapSamples: 30
-
-$namespaces:
- edam: https://edamontology.org/
\ No newline at end of file
diff --git a/runs/shiny/run.cwl b/runs/shiny/run.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..71435f9c300a86f8781e80fa0e7b6b927e8c9da0
--- /dev/null
+++ b/runs/shiny/run.cwl
@@ -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
new file mode 100644
index 0000000000000000000000000000000000000000..1430c8203b6e3d91fc4283c280b3f4aaa2ad374f
--- /dev/null
+++ b/runs/shiny/run.yml
@@ -0,0 +1,4 @@
+in_kallisto_df:
+ class: File
+ path: ../../runs/sleuth/results/kallisto_df.csv
+exp_factor: "Factor..Photosynthesis.mode."
\ No newline at end of file
diff --git a/runs/shiny_plots.Rmd b/runs/shiny_plots.Rmd
deleted file mode 100644
index 3a1e99cf680cdd3c67d2d5d55397db7e39147d13..0000000000000000000000000000000000000000
--- a/runs/shiny_plots.Rmd
+++ /dev/null
@@ -1,77 +0,0 @@
----
-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)
- }),
- )
-)
-```
diff --git a/runs/shiny_prep/out/shiny_prep.RData b/runs/shiny_prep/out/shiny_prep.RData
deleted file mode 100644
index ae56a9cb309ac5e6b27e0c2a7c916035cbcc9dae..0000000000000000000000000000000000000000
Binary files a/runs/shiny_prep/out/shiny_prep.RData and /dev/null differ
diff --git a/runs/shiny_prep/run.cwl b/runs/shiny_prep/run.cwl
deleted file mode 100644
index aa7ea15dbeb66f345b610edc8c2ba3b0043d7851..0000000000000000000000000000000000000000
--- a/runs/shiny_prep/run.cwl
+++ /dev/null
@@ -1,29 +0,0 @@
-#!/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
diff --git a/runs/shiny_prep/run.yml b/runs/shiny_prep/run.yml
deleted file mode 100644
index 8e7954b4766c5dabe9c6c4bac267ad186782abef..0000000000000000000000000000000000000000
--- a/runs/shiny_prep/run.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-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
diff --git a/studies/.gitkeep b/studies/.gitkeep
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/workflows/deseq2/mutli-docker-test.cwl b/workflows/deseq2/mutli-docker-test.cwl
deleted file mode 100644
index 136d87e72742f52c9ac1cdfe287273e5462b541a..0000000000000000000000000000000000000000
--- a/workflows/deseq2/mutli-docker-test.cwl
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/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: []
diff --git a/workflows/shiny/shiny-app.R b/workflows/shiny/shiny-app.R
new file mode 100644
index 0000000000000000000000000000000000000000..4c020248813f9dfe57180989361fa246103f07a7
--- /dev/null
+++ b/workflows/shiny/shiny-app.R
@@ -0,0 +1,68 @@
+#!/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)
diff --git a/workflows/shiny/workflow.cwl b/workflows/shiny/workflow.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..2e80423e1801af7875f5917f15ff4f704afa2c9e
--- /dev/null
+++ b/workflows/shiny/workflow.cwl
@@ -0,0 +1,31 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.2
+class: CommandLineTool
+
+# hints:
+# DockerRequirement:
+# dockerPull:
+
+requirements:
+ - class: InitialWorkDirRequirement
+ listing:
+ - entryname: shiny-app.R
+ entry:
+ $include: shiny-app.R
+ - class: NetworkAccess
+ networkAccess: true
+
+baseCommand: [Rscript, shiny-app.R]
+
+inputs:
+ in_kallisto_df:
+ type: File
+ inputBinding:
+ position: 1
+ exp_factor:
+ type: string
+ inputBinding:
+ position: 2
+
+outputs: []
\ No newline at end of file
diff --git a/workflows/shiny_prep/shiny_prep.R b/workflows/shiny_prep/shiny_prep.R
deleted file mode 100644
index 804ad85db72c912c214f19b868e6073316524bab..0000000000000000000000000000000000000000
--- a/workflows/shiny_prep/shiny_prep.R
+++ /dev/null
@@ -1,26 +0,0 @@
-#!/usr/bin/env Rscript
-
-################################################
-#### Read arguments from CLI
-################################################
-
-args <- commandArgs(trailingOnly = T)
-
-out_folder <- args[1]
-in_kallisto_df <- args[2]
-
-################################################
-#### If it does not exist, create out dir
-################################################
-
-dir.create(out_folder, recursive = T, showWarnings = F)
-
-################################################
-#### Prep data for shiny app
-################################################
-
-expression_data <- read.csv(file = in_kallisto_df)
-
-available_genes <- unique(expression_data$target_id)
-
-save(expression_data, available_genes, file = paste(out_folder, 'shiny_prep.RData', sep = "/"))