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--- a/.gitattributes
+++ b/.gitattributes
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runs/kallisto_index/out/kallisto_index filter=lfs diff=lfs merge=lfs -text
studies/arabidopsis-reference/resources/Arabidopsis_thaliana.TAIR10.28.cdna.all.fa filter=lfs diff=lfs merge=lfs -text
+runs/kallisto_quant-pe/out/50-WT-D_S21_L002/abundance.h5 filter=lfs diff=lfs merge=lfs -text
+runs/kallisto_quant-pe/out/50-WT-D_S21_L002/abundance.tsv filter=lfs diff=lfs merge=lfs -text
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+ "n_bootstraps": 30,
+ "n_processed": 30869744,
+ "kallisto_version": "0.43.0",
+ "index_version": 10,
+ "start_time": "Thu Jan 25 13:20:21 2024",
+ "call": "kallisto quant -b 30 -t 4 -i /var/lib/cwl/stgbd0fc0c0-3b39-4d0b-8c87-5618da767205/kallisto_index -o ./out/50-WT-D_S21_L002 /var/lib/cwl/stg4036b29a-e463-4614-bf7a-fb2f022f00ca/dataset/50-WT-D_S21_L002_R1_001.fastq.gz /var/lib/cwl/stg4036b29a-e463-4614-bf7a-fb2f022f00ca/dataset/50-WT-D_S21_L002_R2_001.fastq.gz"
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+[1;30mINFO[0m /Users/dominikbrilhaus/opt/anaconda3/bin/cwltool 3.1.20240112164112
+[1;30mINFO[0m Resolved 'run.cwl' to 'file:///Users/dominikbrilhaus/gitlab_dataplant/hhu-plant-biochemistry/2018_SamuilovBrilhaus_BOU_DB/runs/kallisto_quant-pe/run.cwl'
+[1;30mINFO[0m [job run.cwl] /private/tmp/docker_tmpbbc44k52$ docker \
+ run \
+ -i \
+ --mount=type=bind,source=/private/tmp/docker_tmpbbc44k52,target=/KHFwkx \
+ --mount=type=bind,source=/private/tmp/docker_tmpaqm0vcus,target=/tmp \
+ --mount=type=bind,source=/Users/dominikbrilhaus/gitlab_dataplant/hhu-plant-biochemistry/2018_SamuilovBrilhaus_BOU_DB/workflows/kallisto_quant-pe/kallisto_quant-pe.sh,target=/var/lib/cwl/stgea2c243e-7dc5-42e1-8073-b054c37b123f/kallisto_quant-pe.sh,readonly \
+ --mount=type=bind,source=/Users/dominikbrilhaus/gitlab_dataplant/hhu-plant-biochemistry/2018_SamuilovBrilhaus_BOU_DB/runs/kallisto_index/out/kallisto_index,target=/var/lib/cwl/stgbd0fc0c0-3b39-4d0b-8c87-5618da767205/kallisto_index,readonly \
+ --mount=type=bind,source=/Users/dominikbrilhaus/gitlab_dataplant/hhu-plant-biochemistry/2018_SamuilovBrilhaus_BOU_DB/assays/rna-seq/dataset,target=/var/lib/cwl/stg4036b29a-e463-4614-bf7a-fb2f022f00ca/dataset,readonly \
+ --workdir=/KHFwkx \
+ --read-only=true \
+ --net=none \
+ --user=502:20 \
+ --rm \
+ --cidfile=/private/tmp/docker_tmprgaby8b9/20240125142021-081142.cid \
+ --env=TMPDIR=/tmp \
+ --env=HOME=/KHFwkx \
+ quay.io/biocontainers/kallisto:0.43.0--hdf51.8.17_2 \
+ bash \
+ /var/lib/cwl/stgea2c243e-7dc5-42e1-8073-b054c37b123f/kallisto_quant-pe.sh \
+ ./out \
+ /var/lib/cwl/stgbd0fc0c0-3b39-4d0b-8c87-5618da767205/kallisto_index \
+ /var/lib/cwl/stg4036b29a-e463-4614-bf7a-fb2f022f00ca/dataset \
+ 30 \
+ 4
+50-WT-D_S21_L002
+
+[quant] fragment length distribution will be estimated from the data
+[index] k-mer length: 31
+[index] number of targets: 41,392
+[index] number of k-mers: 47,713,570
+[index] number of equivalence classes: 115,412
+[quant] running in paired-end mode
+[quant] will process pair 1: /var/lib/cwl/stg4036b29a-e463-4614-bf7a-fb2f022f00ca/dataset/50-WT-D_S21_L002_R1_001.fastq.gz
+ /var/lib/cwl/stg4036b29a-e463-4614-bf7a-fb2f022f00ca/dataset/50-WT-D_S21_L002_R2_001.fastq.gz
+[quant] finding pseudoalignments for the reads ... done
+[quant] processed 30,869,744 reads, 29,573,099 reads pseudoaligned
+[quant] estimated average fragment length: 152.005
+[ em] quantifying the abundances ... done
+[ em] the Expectation-Maximization algorithm ran for 976 rounds
+[bstrp] number of EM bootstraps complete: 1
[bstrp] number of EM bootstraps complete: 2
[bstrp] number of EM bootstraps complete: 3
[bstrp] number of EM bootstraps complete: 4
[bstrp] number of EM bootstraps complete: 5
[bstrp] number of EM bootstraps complete: 6
[bstrp] number of EM bootstraps complete: 7
[bstrp] number of EM bootstraps complete: 8
[bstrp] number of EM bootstraps complete: 9
[bstrp] number of EM bootstraps complete: 10
[bstrp] number of EM bootstraps complete: 11
[bstrp] number of EM bootstraps complete: 12
[bstrp] number of EM bootstraps complete: 13
[bstrp] number of EM bootstraps complete: 14
[bstrp] number of EM bootstraps complete: 15
[bstrp] number of EM bootstraps complete: 16
[bstrp] number of EM bootstraps complete: 17
[bstrp] number of EM bootstraps complete: 18
[bstrp] number of EM bootstraps complete: 19
[bstrp] number of EM bootstraps complete: 20
[bstrp] number of EM bootstraps complete: 21
[bstrp] number of EM bootstraps complete: 22
[bstrp] number of EM bootstraps complete: 23
[bstrp] number of EM bootstraps complete: 24
[bstrp] number of EM bootstraps complete: 25
[bstrp] number of EM bootstraps complete: 26
[bstrp] number of EM bootstraps complete: 27
[bstrp] number of EM bootstraps complete: 28
[bstrp] number of EM bootstraps complete: 29
[bstrp] number of EM bootstraps complete: 30
+
+Kallisto done
+[1;30mINFO[0m [job run.cwl] Max memory used: 3563MiB
+[1;30mINFO[0m [job run.cwl] completed success
+{
+ "outdir": [
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+ "class": "Directory",
+ "listing": [
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+ "basename": "50-WT-D_S21_L002",
+ "listing": [
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+ },
+ {
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+ "checksum": "sha1$f95cf34e2552f95328cc0438b1285b0b23cc275c",
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+ },
+ {
+ "class": "File",
+ "location": "file:///Users/dominikbrilhaus/gitlab_dataplant/hhu-plant-biochemistry/2018_SamuilovBrilhaus_BOU_DB/runs/kallisto_quant-pe/out/50-WT-D_S21_L002/abundance.h5",
+ "basename": "abundance.h5",
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+ "checksum": "sha1$7a3e30ab39c7a84f98673e41e633b288866bd5f2",
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+ }
+ ],
+ "path": "/Users/dominikbrilhaus/gitlab_dataplant/hhu-plant-biochemistry/2018_SamuilovBrilhaus_BOU_DB/runs/kallisto_quant-pe/out/50-WT-D_S21_L002"
+ }
+ ],
+ "path": "/Users/dominikbrilhaus/gitlab_dataplant/hhu-plant-biochemistry/2018_SamuilovBrilhaus_BOU_DB/runs/kallisto_quant-pe/out"
+ }
+ ]
+}[1;30mINFO[0m Final process status is success