From 163979ffe84e4649b85566aad761da7c0d185e64 Mon Sep 17 00:00:00 2001
From: Dominik Brilhaus <brilhaus@nfdi4plants.org>
Date: Fri, 2 Aug 2024 10:06:36 +0200
Subject: [PATCH] remove old scripts, cwl approaches, run results
---
assays/.gitkeep | 0
runs/.gitkeep | 0
runs/kallisto_index/out/kallisto_index | 3 -
runs/kallisto_index/run.cwl | 29 -
.../abundance.h5 | 3 -
.../abundance.tsv | 31435 ----------------
.../run_info.json | 13 -
.../abundance.h5 | 3 -
.../abundance.tsv | 31435 ----------------
.../run_info.json | 13 -
.../abundance.h5 | 3 -
.../abundance.tsv | 31435 ----------------
.../run_info.json | 13 -
.../abundance.h5 | 3 -
.../abundance.tsv | 31435 ----------------
.../run_info.json | 13 -
.../abundance.h5 | 3 -
.../abundance.tsv | 31435 ----------------
.../run_info.json | 13 -
.../abundance.h5 | 3 -
.../abundance.tsv | 31435 ----------------
.../run_info.json | 13 -
runs/kallisto_quant/run.cwl | 49 -
studies/.gitkeep | 0
workflows/.gitkeep | 0
workflows/kallisto_index/kallisto_index.sh | 29 -
workflows/kallisto_quant/kallisto_quant.sh | 44 -
27 files changed, 188860 deletions(-)
delete mode 100644 assays/.gitkeep
delete mode 100644 runs/.gitkeep
delete mode 100644 runs/kallisto_index/out/kallisto_index
delete mode 100644 runs/kallisto_index/run.cwl
delete mode 100644 runs/kallisto_quant/kallisto_results/DB_097_CAMMD_CAGATC_L001_R1_001/abundance.h5
delete mode 100644 runs/kallisto_quant/kallisto_results/DB_097_CAMMD_CAGATC_L001_R1_001/abundance.tsv
delete mode 100644 runs/kallisto_quant/kallisto_results/DB_097_CAMMD_CAGATC_L001_R1_001/run_info.json
delete mode 100644 runs/kallisto_quant/kallisto_results/DB_099_CAMMD_CTTGTA_L001_R1_001/abundance.h5
delete mode 100644 runs/kallisto_quant/kallisto_results/DB_099_CAMMD_CTTGTA_L001_R1_001/abundance.tsv
delete mode 100644 runs/kallisto_quant/kallisto_results/DB_099_CAMMD_CTTGTA_L001_R1_001/run_info.json
delete mode 100644 runs/kallisto_quant/kallisto_results/DB_103_CAMMD_AGTCAA_L001_R1_001/abundance.h5
delete mode 100644 runs/kallisto_quant/kallisto_results/DB_103_CAMMD_AGTCAA_L001_R1_001/abundance.tsv
delete mode 100644 runs/kallisto_quant/kallisto_results/DB_103_CAMMD_AGTCAA_L001_R1_001/run_info.json
delete mode 100644 runs/kallisto_quant/kallisto_results/DB_161_reC3MD_GTCCGC_L001_R1_001/abundance.h5
delete mode 100644 runs/kallisto_quant/kallisto_results/DB_161_reC3MD_GTCCGC_L001_R1_001/abundance.tsv
delete mode 100644 runs/kallisto_quant/kallisto_results/DB_161_reC3MD_GTCCGC_L001_R1_001/run_info.json
delete mode 100644 runs/kallisto_quant/kallisto_results/DB_163_reC3MD_GTGAAA_L001_R1_001/abundance.h5
delete mode 100644 runs/kallisto_quant/kallisto_results/DB_163_reC3MD_GTGAAA_L001_R1_001/abundance.tsv
delete mode 100644 runs/kallisto_quant/kallisto_results/DB_163_reC3MD_GTGAAA_L001_R1_001/run_info.json
delete mode 100644 runs/kallisto_quant/kallisto_results/DB_165_re-C3MD_GTGAAA_L002_R1_001/abundance.h5
delete mode 100644 runs/kallisto_quant/kallisto_results/DB_165_re-C3MD_GTGAAA_L002_R1_001/abundance.tsv
delete mode 100644 runs/kallisto_quant/kallisto_results/DB_165_re-C3MD_GTGAAA_L002_R1_001/run_info.json
delete mode 100644 runs/kallisto_quant/run.cwl
delete mode 100644 studies/.gitkeep
delete mode 100644 workflows/.gitkeep
delete mode 100644 workflows/kallisto_index/kallisto_index.sh
delete mode 100644 workflows/kallisto_quant/kallisto_quant.sh
diff --git a/assays/.gitkeep b/assays/.gitkeep
deleted file mode 100644
index e69de29..0000000
diff --git a/runs/.gitkeep b/runs/.gitkeep
deleted file mode 100644
index e69de29..0000000
diff --git a/runs/kallisto_index/out/kallisto_index b/runs/kallisto_index/out/kallisto_index
deleted file mode 100644
index f269712..0000000
--- a/runs/kallisto_index/out/kallisto_index
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:179d159502ea85576e5028a32e698c44c1bb076602e17de09f62b9a9b937f8d7
-size 750438441
diff --git a/runs/kallisto_index/run.cwl b/runs/kallisto_index/run.cwl
deleted file mode 100644
index a8665ac..0000000
--- a/runs/kallisto_index/run.cwl
+++ /dev/null
@@ -1,29 +0,0 @@
-#!/usr/bin/env cwl-runner
-
-cwlVersion: v1.2
-class: CommandLineTool
-
-inputs:
-- id: sh_script
- type: File
- inputBinding:
- position: 0
-- id: in_genome_ref
- type: File
- inputBinding:
- position: 2
-- id: out_folder
- type: string
- inputBinding:
- position: 3
-
-outputs:
-- id: outdir
- type:
- type: array
- items: Directory
- outputBinding:
- glob: $(runtime.outdir)/$(inputs.out_folder)
-
-baseCommand:
-- bash
diff --git a/runs/kallisto_quant/kallisto_results/DB_097_CAMMD_CAGATC_L001_R1_001/abundance.h5 b/runs/kallisto_quant/kallisto_results/DB_097_CAMMD_CAGATC_L001_R1_001/abundance.h5
deleted file mode 100644
index 91ad581..0000000
--- a/runs/kallisto_quant/kallisto_results/DB_097_CAMMD_CAGATC_L001_R1_001/abundance.h5
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:44c51c59dcf75639923ac44606f656dde5567ca50976b21c9181d53f8419635f
-size 6259639
diff --git a/runs/kallisto_quant/kallisto_results/DB_097_CAMMD_CAGATC_L001_R1_001/abundance.tsv b/runs/kallisto_quant/kallisto_results/DB_097_CAMMD_CAGATC_L001_R1_001/abundance.tsv
deleted file mode 100644
index 1189cbc..0000000
--- a/runs/kallisto_quant/kallisto_results/DB_097_CAMMD_CAGATC_L001_R1_001/abundance.tsv
+++ /dev/null
@@ -1,31435 +0,0 @@
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diff --git a/runs/kallisto_quant/kallisto_results/DB_097_CAMMD_CAGATC_L001_R1_001/run_info.json b/runs/kallisto_quant/kallisto_results/DB_097_CAMMD_CAGATC_L001_R1_001/run_info.json
deleted file mode 100644
index 5cf4939..0000000
--- a/runs/kallisto_quant/kallisto_results/DB_097_CAMMD_CAGATC_L001_R1_001/run_info.json
+++ /dev/null
@@ -1,13 +0,0 @@
-{
- "n_targets": 31434,
- "n_bootstraps": 100,
- "n_processed": 11071656,
- "n_pseudoaligned": 7663654,
- "n_unique": 7522185,
- "p_pseudoaligned": 69.2,
- "p_unique": 67.9,
- "kallisto_version": "0.48.0",
- "index_version": 10,
- "start_time": "Wed Aug 10 18:21:29 2022",
- "call": "kallisto quant --single -b 100 -t 4 -l 200 -s 20 -i /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/runs/kallisto_index/kallisto_index -o /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/runs/kallisto_quant/kallisto_results/DB_097_CAMMD_CAGATC_L001_R1_001 /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/assays/Talinum_RNASeq_minimal/dataset/DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz"
-}
diff --git a/runs/kallisto_quant/kallisto_results/DB_099_CAMMD_CTTGTA_L001_R1_001/abundance.h5 b/runs/kallisto_quant/kallisto_results/DB_099_CAMMD_CTTGTA_L001_R1_001/abundance.h5
deleted file mode 100644
index 47ed7ef..0000000
--- a/runs/kallisto_quant/kallisto_results/DB_099_CAMMD_CTTGTA_L001_R1_001/abundance.h5
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
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diff --git a/runs/kallisto_quant/kallisto_results/DB_099_CAMMD_CTTGTA_L001_R1_001/abundance.tsv b/runs/kallisto_quant/kallisto_results/DB_099_CAMMD_CTTGTA_L001_R1_001/abundance.tsv
deleted file mode 100644
index 1668d50..0000000
--- a/runs/kallisto_quant/kallisto_results/DB_099_CAMMD_CTTGTA_L001_R1_001/abundance.tsv
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diff --git a/runs/kallisto_quant/kallisto_results/DB_099_CAMMD_CTTGTA_L001_R1_001/run_info.json b/runs/kallisto_quant/kallisto_results/DB_099_CAMMD_CTTGTA_L001_R1_001/run_info.json
deleted file mode 100644
index 7eb4f4d..0000000
--- a/runs/kallisto_quant/kallisto_results/DB_099_CAMMD_CTTGTA_L001_R1_001/run_info.json
+++ /dev/null
@@ -1,13 +0,0 @@
-{
- "n_targets": 31434,
- "n_bootstraps": 100,
- "n_processed": 14332278,
- "n_pseudoaligned": 10066506,
- "n_unique": 9848811,
- "p_pseudoaligned": 70.2,
- "p_unique": 68.7,
- "kallisto_version": "0.48.0",
- "index_version": 10,
- "start_time": "Wed Aug 10 18:22:23 2022",
- "call": "kallisto quant --single -b 100 -t 4 -l 200 -s 20 -i /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/runs/kallisto_index/kallisto_index -o /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/runs/kallisto_quant/kallisto_results/DB_099_CAMMD_CTTGTA_L001_R1_001 /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/assays/Talinum_RNASeq_minimal/dataset/DB_099_CAMMD_CTTGTA_L001_R1_001.fastq.gz"
-}
diff --git a/runs/kallisto_quant/kallisto_results/DB_103_CAMMD_AGTCAA_L001_R1_001/abundance.h5 b/runs/kallisto_quant/kallisto_results/DB_103_CAMMD_AGTCAA_L001_R1_001/abundance.h5
deleted file mode 100644
index b737326..0000000
--- a/runs/kallisto_quant/kallisto_results/DB_103_CAMMD_AGTCAA_L001_R1_001/abundance.h5
+++ /dev/null
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deleted file mode 100644
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diff --git a/runs/kallisto_quant/kallisto_results/DB_103_CAMMD_AGTCAA_L001_R1_001/run_info.json b/runs/kallisto_quant/kallisto_results/DB_103_CAMMD_AGTCAA_L001_R1_001/run_info.json
deleted file mode 100644
index 7769844..0000000
--- a/runs/kallisto_quant/kallisto_results/DB_103_CAMMD_AGTCAA_L001_R1_001/run_info.json
+++ /dev/null
@@ -1,13 +0,0 @@
-{
- "n_targets": 31434,
- "n_bootstraps": 100,
- "n_processed": 13083957,
- "n_pseudoaligned": 9007720,
- "n_unique": 8828236,
- "p_pseudoaligned": 68.8,
- "p_unique": 67.5,
- "kallisto_version": "0.48.0",
- "index_version": 10,
- "start_time": "Wed Aug 10 18:23:36 2022",
- "call": "kallisto quant --single -b 100 -t 4 -l 200 -s 20 -i /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/runs/kallisto_index/kallisto_index -o /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/runs/kallisto_quant/kallisto_results/DB_103_CAMMD_AGTCAA_L001_R1_001 /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/assays/Talinum_RNASeq_minimal/dataset/DB_103_CAMMD_AGTCAA_L001_R1_001.fastq.gz"
-}
diff --git a/runs/kallisto_quant/kallisto_results/DB_161_reC3MD_GTCCGC_L001_R1_001/abundance.h5 b/runs/kallisto_quant/kallisto_results/DB_161_reC3MD_GTCCGC_L001_R1_001/abundance.h5
deleted file mode 100644
index a73f601..0000000
--- a/runs/kallisto_quant/kallisto_results/DB_161_reC3MD_GTCCGC_L001_R1_001/abundance.h5
+++ /dev/null
@@ -1,3 +0,0 @@
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diff --git a/runs/kallisto_quant/kallisto_results/DB_161_reC3MD_GTCCGC_L001_R1_001/abundance.tsv b/runs/kallisto_quant/kallisto_results/DB_161_reC3MD_GTCCGC_L001_R1_001/abundance.tsv
deleted file mode 100644
index c0ce029..0000000
--- a/runs/kallisto_quant/kallisto_results/DB_161_reC3MD_GTCCGC_L001_R1_001/abundance.tsv
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diff --git a/runs/kallisto_quant/kallisto_results/DB_161_reC3MD_GTCCGC_L001_R1_001/run_info.json b/runs/kallisto_quant/kallisto_results/DB_161_reC3MD_GTCCGC_L001_R1_001/run_info.json
deleted file mode 100644
index 600b369..0000000
--- a/runs/kallisto_quant/kallisto_results/DB_161_reC3MD_GTCCGC_L001_R1_001/run_info.json
+++ /dev/null
@@ -1,13 +0,0 @@
-{
- "n_targets": 31434,
- "n_bootstraps": 100,
- "n_processed": 12785081,
- "n_pseudoaligned": 9058396,
- "n_unique": 8740183,
- "p_pseudoaligned": 70.9,
- "p_unique": 68.4,
- "kallisto_version": "0.48.0",
- "index_version": 10,
- "start_time": "Wed Aug 10 18:24:45 2022",
- "call": "kallisto quant --single -b 100 -t 4 -l 200 -s 20 -i /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/runs/kallisto_index/kallisto_index -o /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/runs/kallisto_quant/kallisto_results/DB_161_reC3MD_GTCCGC_L001_R1_001 /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/assays/Talinum_RNASeq_minimal/dataset/DB_161_reC3MD_GTCCGC_L001_R1_001.fastq.gz"
-}
diff --git a/runs/kallisto_quant/kallisto_results/DB_163_reC3MD_GTGAAA_L001_R1_001/abundance.h5 b/runs/kallisto_quant/kallisto_results/DB_163_reC3MD_GTGAAA_L001_R1_001/abundance.h5
deleted file mode 100644
index 23ad7a3..0000000
--- a/runs/kallisto_quant/kallisto_results/DB_163_reC3MD_GTGAAA_L001_R1_001/abundance.h5
+++ /dev/null
@@ -1,3 +0,0 @@
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diff --git a/runs/kallisto_quant/kallisto_results/DB_163_reC3MD_GTGAAA_L001_R1_001/abundance.tsv b/runs/kallisto_quant/kallisto_results/DB_163_reC3MD_GTGAAA_L001_R1_001/abundance.tsv
deleted file mode 100644
index 4a165bf..0000000
--- a/runs/kallisto_quant/kallisto_results/DB_163_reC3MD_GTGAAA_L001_R1_001/abundance.tsv
+++ /dev/null
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diff --git a/runs/kallisto_quant/kallisto_results/DB_163_reC3MD_GTGAAA_L001_R1_001/run_info.json b/runs/kallisto_quant/kallisto_results/DB_163_reC3MD_GTGAAA_L001_R1_001/run_info.json
deleted file mode 100644
index 50be24a..0000000
--- a/runs/kallisto_quant/kallisto_results/DB_163_reC3MD_GTGAAA_L001_R1_001/run_info.json
+++ /dev/null
@@ -1,13 +0,0 @@
-{
- "n_targets": 31434,
- "n_bootstraps": 100,
- "n_processed": 14312514,
- "n_pseudoaligned": 10054493,
- "n_unique": 9707941,
- "p_pseudoaligned": 70.2,
- "p_unique": 67.8,
- "kallisto_version": "0.48.0",
- "index_version": 10,
- "start_time": "Wed Aug 10 18:25:50 2022",
- "call": "kallisto quant --single -b 100 -t 4 -l 200 -s 20 -i /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/runs/kallisto_index/kallisto_index -o /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/runs/kallisto_quant/kallisto_results/DB_163_reC3MD_GTGAAA_L001_R1_001 /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/assays/Talinum_RNASeq_minimal/dataset/DB_163_reC3MD_GTGAAA_L001_R1_001.fastq.gz"
-}
diff --git a/runs/kallisto_quant/kallisto_results/DB_165_re-C3MD_GTGAAA_L002_R1_001/abundance.h5 b/runs/kallisto_quant/kallisto_results/DB_165_re-C3MD_GTGAAA_L002_R1_001/abundance.h5
deleted file mode 100644
index b2066fa..0000000
--- a/runs/kallisto_quant/kallisto_results/DB_165_re-C3MD_GTGAAA_L002_R1_001/abundance.h5
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:b22c4facc6705596e01e28b6bf7f9923667ce19b18cf0204d3c75a18fab642fc
-size 6741837
diff --git a/runs/kallisto_quant/kallisto_results/DB_165_re-C3MD_GTGAAA_L002_R1_001/abundance.tsv b/runs/kallisto_quant/kallisto_results/DB_165_re-C3MD_GTGAAA_L002_R1_001/abundance.tsv
deleted file mode 100644
index 884c56f..0000000
--- a/runs/kallisto_quant/kallisto_results/DB_165_re-C3MD_GTGAAA_L002_R1_001/abundance.tsv
+++ /dev/null
@@ -1,31435 +0,0 @@
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diff --git a/runs/kallisto_quant/kallisto_results/DB_165_re-C3MD_GTGAAA_L002_R1_001/run_info.json b/runs/kallisto_quant/kallisto_results/DB_165_re-C3MD_GTGAAA_L002_R1_001/run_info.json
deleted file mode 100644
index 599182d..0000000
--- a/runs/kallisto_quant/kallisto_results/DB_165_re-C3MD_GTGAAA_L002_R1_001/run_info.json
+++ /dev/null
@@ -1,13 +0,0 @@
-{
- "n_targets": 31434,
- "n_bootstraps": 100,
- "n_processed": 13679479,
- "n_pseudoaligned": 9552504,
- "n_unique": 9264346,
- "p_pseudoaligned": 69.8,
- "p_unique": 67.7,
- "kallisto_version": "0.48.0",
- "index_version": 10,
- "start_time": "Wed Aug 10 18:26:59 2022",
- "call": "kallisto quant --single -b 100 -t 4 -l 200 -s 20 -i /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/runs/kallisto_index/kallisto_index -o /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/runs/kallisto_quant/kallisto_results/DB_165_re-C3MD_GTGAAA_L002_R1_001 /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/assays/Talinum_RNASeq_minimal/dataset/DB_165_re-C3MD_GTGAAA_L002_R1_001.fastq.gz"
-}
diff --git a/runs/kallisto_quant/run.cwl b/runs/kallisto_quant/run.cwl
deleted file mode 100644
index 980dc14..0000000
--- a/runs/kallisto_quant/run.cwl
+++ /dev/null
@@ -1,49 +0,0 @@
-#!/usr/bin/env cwl-runner
-
-cwlVersion: v1.2
-class: CommandLineTool
-
-inputs:
-- id: sh_script
- type: File
- inputBinding:
- position: 0
-- id: out_folder
- type: string
- inputBinding:
- position: 1
-- id: in_kallisto_index
- type: File
- inputBinding:
- position: 2
-- id: in_fastq_dir
- type: Directory
- inputBinding:
- position: 3
-- id: kallisto_bootstrap
- type: int
- inputBinding:
- position: 4
-- id: kallisto_threads
- type: int
- inputBinding:
- position: 5
-- id: kallisto_fragmentLength
- type: int
- inputBinding:
- position: 6
-- id: kallisto_stdDev
- type: int
- inputBinding:
- position: 7
-
-outputs:
-- id: outdir
- type:
- type: array
- items: Directory
- outputBinding:
- glob: $(runtime.outdir)/$(inputs.out_folder)
-
-baseCommand:
-- bash
diff --git a/studies/.gitkeep b/studies/.gitkeep
deleted file mode 100644
index e69de29..0000000
diff --git a/workflows/.gitkeep b/workflows/.gitkeep
deleted file mode 100644
index e69de29..0000000
diff --git a/workflows/kallisto_index/kallisto_index.sh b/workflows/kallisto_index/kallisto_index.sh
deleted file mode 100644
index c346206..0000000
--- a/workflows/kallisto_index/kallisto_index.sh
+++ /dev/null
@@ -1,29 +0,0 @@
-#!/usr/bin/env bash
-
-### Build kallisto index
-
-################################################
-#### Read arguments from CLI
-################################################
-
-in_genome_ref=$1
-out_folder=$2
-
-################################################
-#### Print version and citation to test kallisto
-################################################
-
-kallisto version
-kallisto cite
-
-################################################
-#### If it does not exist, create out dir
-################################################
-
-mkdir -p $out_folder
-
-################################################
-#### Build kallisto index
-################################################
-
-kallisto index -i $out_folder/kallisto_index $in_genome_ref
diff --git a/workflows/kallisto_quant/kallisto_quant.sh b/workflows/kallisto_quant/kallisto_quant.sh
deleted file mode 100644
index 63d0cb1..0000000
--- a/workflows/kallisto_quant/kallisto_quant.sh
+++ /dev/null
@@ -1,44 +0,0 @@
-#!/usr/bin/env bash
-
-### Map RNASeq reads via kallisto
-### Note, this is written for single-end mode only
-
-################################################
-#### Read arguments from CLI
-################################################
-
-out_folder=$1
-in_kallisto_index=$2
-in_fastq_folder=$3
-kallisto_bootstrap=$4
-kallisto_threads=$5
-kallisto_fragmentLength=$6
-kallisto_stdDev=$7
-
-################################################
-#### If it does not exist, create out dir
-################################################
-
-mkdir -p "$out_folder"
-
-################################################
-#### Store fastq files in variable
-################################################
-
-fastq_files=$(ls "${in_fastq_folder}"/*fastq*)
-
-################################################
-#### Loop over fastq files and quantify reads
-################################################
-
-for j in $fastq_files; do
-
- sampleName=$(basename $j)
-
- echo $sampleName
-
- kallisto quant --single -b $kallisto_bootstrap -t $kallisto_threads -l $kallisto_fragmentLength -s $kallisto_stdDev -i "$in_kallisto_index" -o "$out_folder/$sampleName" $j
-
- echo 'Kallisto done'
-
-done
--
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