From 449cda9208e84dc5d23db2fbf0cd9f156bb99963 Mon Sep 17 00:00:00 2001
From: Dominik Brilhaus <brilhaus@nfdi4plants.org>
Date: Mon, 5 Aug 2024 14:26:09 +0200
Subject: [PATCH] re-run kallisto with v 0.50

---
 runs/kallisto/kallisto_results/DB_097/abundance.h5  | 4 ++--
 runs/kallisto/kallisto_results/DB_097/abundance.tsv | 4 ++--
 runs/kallisto/kallisto_results/DB_097/run_info.json | 2 +-
 runs/kallisto/kallisto_results/DB_099/abundance.h5  | 4 ++--
 runs/kallisto/kallisto_results/DB_099/abundance.tsv | 4 ++--
 runs/kallisto/kallisto_results/DB_099/run_info.json | 2 +-
 runs/kallisto/kallisto_results/DB_103/abundance.h5  | 4 ++--
 runs/kallisto/kallisto_results/DB_103/abundance.tsv | 4 ++--
 runs/kallisto/kallisto_results/DB_103/run_info.json | 2 +-
 runs/kallisto/kallisto_results/DB_161/abundance.h5  | 4 ++--
 runs/kallisto/kallisto_results/DB_161/abundance.tsv | 4 ++--
 runs/kallisto/kallisto_results/DB_161/run_info.json | 2 +-
 runs/kallisto/kallisto_results/DB_163/abundance.h5  | 4 ++--
 runs/kallisto/kallisto_results/DB_163/abundance.tsv | 4 ++--
 runs/kallisto/kallisto_results/DB_163/run_info.json | 2 +-
 runs/kallisto/kallisto_results/DB_165/abundance.h5  | 4 ++--
 runs/kallisto/kallisto_results/DB_165/abundance.tsv | 4 ++--
 runs/kallisto/kallisto_results/DB_165/run_info.json | 2 +-
 runs/kallisto/workflow.yml                          | 2 +-
 19 files changed, 31 insertions(+), 31 deletions(-)

diff --git a/runs/kallisto/kallisto_results/DB_097/abundance.h5 b/runs/kallisto/kallisto_results/DB_097/abundance.h5
index 690e830..eaa773f 100644
--- a/runs/kallisto/kallisto_results/DB_097/abundance.h5
+++ b/runs/kallisto/kallisto_results/DB_097/abundance.h5
@@ -1,3 +1,3 @@
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+size 2093580
diff --git a/runs/kallisto/kallisto_results/DB_097/abundance.tsv b/runs/kallisto/kallisto_results/DB_097/abundance.tsv
index ae069b3..71d9526 100644
--- a/runs/kallisto/kallisto_results/DB_097/abundance.tsv
+++ b/runs/kallisto/kallisto_results/DB_097/abundance.tsv
@@ -1,3 +1,3 @@
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-size 943885
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diff --git a/runs/kallisto/kallisto_results/DB_097/run_info.json b/runs/kallisto/kallisto_results/DB_097/run_info.json
index 96eae87..025fe8d 100644
--- a/runs/kallisto/kallisto_results/DB_097/run_info.json
+++ b/runs/kallisto/kallisto_results/DB_097/run_info.json
@@ -1,3 +1,3 @@
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 size 559
diff --git a/runs/kallisto/kallisto_results/DB_099/abundance.h5 b/runs/kallisto/kallisto_results/DB_099/abundance.h5
index 834d613..f6ae02e 100644
--- a/runs/kallisto/kallisto_results/DB_099/abundance.h5
+++ b/runs/kallisto/kallisto_results/DB_099/abundance.h5
@@ -1,3 +1,3 @@
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+size 2161215
diff --git a/runs/kallisto/kallisto_results/DB_099/abundance.tsv b/runs/kallisto/kallisto_results/DB_099/abundance.tsv
index b8fa7ab..382fca1 100644
--- a/runs/kallisto/kallisto_results/DB_099/abundance.tsv
+++ b/runs/kallisto/kallisto_results/DB_099/abundance.tsv
@@ -1,3 +1,3 @@
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diff --git a/runs/kallisto/kallisto_results/DB_099/run_info.json b/runs/kallisto/kallisto_results/DB_099/run_info.json
index f6bbfd4..6349193 100644
--- a/runs/kallisto/kallisto_results/DB_099/run_info.json
+++ b/runs/kallisto/kallisto_results/DB_099/run_info.json
@@ -1,3 +1,3 @@
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diff --git a/runs/kallisto/kallisto_results/DB_103/abundance.h5 b/runs/kallisto/kallisto_results/DB_103/abundance.h5
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--- a/runs/kallisto/kallisto_results/DB_103/abundance.h5
+++ b/runs/kallisto/kallisto_results/DB_103/abundance.h5
@@ -1,3 +1,3 @@
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-size 2137414
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+size 2137744
diff --git a/runs/kallisto/kallisto_results/DB_103/abundance.tsv b/runs/kallisto/kallisto_results/DB_103/abundance.tsv
index 47ceb40..e21b58a 100644
--- a/runs/kallisto/kallisto_results/DB_103/abundance.tsv
+++ b/runs/kallisto/kallisto_results/DB_103/abundance.tsv
@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
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-size 947778
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+size 947904
diff --git a/runs/kallisto/kallisto_results/DB_103/run_info.json b/runs/kallisto/kallisto_results/DB_103/run_info.json
index d8f9ab4..c9a3f26 100644
--- a/runs/kallisto/kallisto_results/DB_103/run_info.json
+++ b/runs/kallisto/kallisto_results/DB_103/run_info.json
@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
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 size 559
diff --git a/runs/kallisto/kallisto_results/DB_161/abundance.h5 b/runs/kallisto/kallisto_results/DB_161/abundance.h5
index bf98887..9c791bd 100644
--- a/runs/kallisto/kallisto_results/DB_161/abundance.h5
+++ b/runs/kallisto/kallisto_results/DB_161/abundance.h5
@@ -1,3 +1,3 @@
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+size 2146470
diff --git a/runs/kallisto/kallisto_results/DB_161/abundance.tsv b/runs/kallisto/kallisto_results/DB_161/abundance.tsv
index 88be493..2c512c0 100644
--- a/runs/kallisto/kallisto_results/DB_161/abundance.tsv
+++ b/runs/kallisto/kallisto_results/DB_161/abundance.tsv
@@ -1,3 +1,3 @@
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diff --git a/runs/kallisto/kallisto_results/DB_161/run_info.json b/runs/kallisto/kallisto_results/DB_161/run_info.json
index 2f385f9..0ede011 100644
--- a/runs/kallisto/kallisto_results/DB_161/run_info.json
+++ b/runs/kallisto/kallisto_results/DB_161/run_info.json
@@ -1,3 +1,3 @@
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diff --git a/runs/kallisto/kallisto_results/DB_163/abundance.h5 b/runs/kallisto/kallisto_results/DB_163/abundance.h5
index 69e55e6..754399e 100644
--- a/runs/kallisto/kallisto_results/DB_163/abundance.h5
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@@ -1,3 +1,3 @@
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diff --git a/runs/kallisto/kallisto_results/DB_163/abundance.tsv b/runs/kallisto/kallisto_results/DB_163/abundance.tsv
index 35cc6cd..3bb7c88 100644
--- a/runs/kallisto/kallisto_results/DB_163/abundance.tsv
+++ b/runs/kallisto/kallisto_results/DB_163/abundance.tsv
@@ -1,3 +1,3 @@
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diff --git a/runs/kallisto/kallisto_results/DB_163/run_info.json b/runs/kallisto/kallisto_results/DB_163/run_info.json
index bf3b12b..a073a80 100644
--- a/runs/kallisto/kallisto_results/DB_163/run_info.json
+++ b/runs/kallisto/kallisto_results/DB_163/run_info.json
@@ -1,3 +1,3 @@
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 size 561
diff --git a/runs/kallisto/kallisto_results/DB_165/abundance.h5 b/runs/kallisto/kallisto_results/DB_165/abundance.h5
index add4279..cb080c3 100644
--- a/runs/kallisto/kallisto_results/DB_165/abundance.h5
+++ b/runs/kallisto/kallisto_results/DB_165/abundance.h5
@@ -1,3 +1,3 @@
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+size 2239053
diff --git a/runs/kallisto/kallisto_results/DB_165/abundance.tsv b/runs/kallisto/kallisto_results/DB_165/abundance.tsv
index 2be2791..98040dd 100644
--- a/runs/kallisto/kallisto_results/DB_165/abundance.tsv
+++ b/runs/kallisto/kallisto_results/DB_165/abundance.tsv
@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
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-size 958459
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+size 958283
diff --git a/runs/kallisto/kallisto_results/DB_165/run_info.json b/runs/kallisto/kallisto_results/DB_165/run_info.json
index 0f49f0c..f64d715 100644
--- a/runs/kallisto/kallisto_results/DB_165/run_info.json
+++ b/runs/kallisto/kallisto_results/DB_165/run_info.json
@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:2d0c9832b35d573854206150cdac98d42aa82966041235d46e2a91d9f0ecac8a
+oid sha256:42fa5b9c6df5c1b770339aa8cceec7a0276e8875c79cc639f7ea024f88af2434
 size 561
diff --git a/runs/kallisto/workflow.yml b/runs/kallisto/workflow.yml
index 21d672d..0f8f15d 100644
--- a/runs/kallisto/workflow.yml
+++ b/runs/kallisto/workflow.yml
@@ -34,7 +34,7 @@ InputReadsMultipleSamples:
       path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_165_re-C3MD_GTGAAA_L002_R1_001.fastq.gz
       format: edam:format_1930 # FASTQ
 
-numUnderscoresFileName: 1
+numUnderscoresFileName: 2
 
 ### Kallisto quant Parameters
 isSingle: true
-- 
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