From dd14c78d6830b14f03eafbb37b72675db16390cc Mon Sep 17 00:00:00 2001 From: Robert Syme Date: Sun, 17 Nov 2024 21:18:57 +0000 Subject: [PATCH 1/7] Remove executable permission from nextflow scripts in hello nextflow --- hello-nextflow/hello-genomics.nf | 0 hello-nextflow/hello-world.nf | 0 hello-nextflow/solutions/hello-world/hello-world-1.nf | 0 hello-nextflow/solutions/hello-world/hello-world-2.nf | 0 hello-nextflow/solutions/hello-world/hello-world-3.nf | 0 hello-nextflow/solutions/hello-world/hello-world-4.nf | 0 hello-nextflow/solutions/hello-world/hello-world-5.nf | 0 hello-nextflow/solutions/hello-world/hello-world-6.nf | 0 hello-nextflow/solutions/hello-world/hello-world-7.nf | 0 hello-nextflow/solutions/hello-world/hello-world-8.nf | 0 hello-nextflow/solutions/hello-world/hello-world-9.nf | 0 11 files changed, 0 insertions(+), 0 deletions(-) mode change 100755 => 100644 hello-nextflow/hello-genomics.nf mode change 100755 => 100644 hello-nextflow/hello-world.nf mode change 100755 => 100644 hello-nextflow/solutions/hello-world/hello-world-1.nf mode change 100755 => 100644 hello-nextflow/solutions/hello-world/hello-world-2.nf mode change 100755 => 100644 hello-nextflow/solutions/hello-world/hello-world-3.nf mode change 100755 => 100644 hello-nextflow/solutions/hello-world/hello-world-4.nf mode change 100755 => 100644 hello-nextflow/solutions/hello-world/hello-world-5.nf mode change 100755 => 100644 hello-nextflow/solutions/hello-world/hello-world-6.nf mode change 100755 => 100644 hello-nextflow/solutions/hello-world/hello-world-7.nf mode change 100755 => 100644 hello-nextflow/solutions/hello-world/hello-world-8.nf mode change 100755 => 100644 hello-nextflow/solutions/hello-world/hello-world-9.nf diff --git a/hello-nextflow/hello-genomics.nf b/hello-nextflow/hello-genomics.nf old mode 100755 new mode 100644 diff --git a/hello-nextflow/hello-world.nf b/hello-nextflow/hello-world.nf old mode 100755 new mode 100644 diff --git a/hello-nextflow/solutions/hello-world/hello-world-1.nf b/hello-nextflow/solutions/hello-world/hello-world-1.nf old mode 100755 new mode 100644 diff --git a/hello-nextflow/solutions/hello-world/hello-world-2.nf b/hello-nextflow/solutions/hello-world/hello-world-2.nf old mode 100755 new mode 100644 diff --git a/hello-nextflow/solutions/hello-world/hello-world-3.nf b/hello-nextflow/solutions/hello-world/hello-world-3.nf old mode 100755 new mode 100644 diff --git a/hello-nextflow/solutions/hello-world/hello-world-4.nf b/hello-nextflow/solutions/hello-world/hello-world-4.nf old mode 100755 new mode 100644 diff --git a/hello-nextflow/solutions/hello-world/hello-world-5.nf b/hello-nextflow/solutions/hello-world/hello-world-5.nf old mode 100755 new mode 100644 diff --git a/hello-nextflow/solutions/hello-world/hello-world-6.nf b/hello-nextflow/solutions/hello-world/hello-world-6.nf old mode 100755 new mode 100644 diff --git a/hello-nextflow/solutions/hello-world/hello-world-7.nf b/hello-nextflow/solutions/hello-world/hello-world-7.nf old mode 100755 new mode 100644 diff --git a/hello-nextflow/solutions/hello-world/hello-world-8.nf b/hello-nextflow/solutions/hello-world/hello-world-8.nf old mode 100755 new mode 100644 diff --git a/hello-nextflow/solutions/hello-world/hello-world-9.nf b/hello-nextflow/solutions/hello-world/hello-world-9.nf old mode 100755 new mode 100644 From f28a977c1fa5e5a24d627afc4a4731bc10f80ac9 Mon Sep 17 00:00:00 2001 From: Robert Syme Date: Sun, 17 Nov 2024 21:20:19 +0000 Subject: [PATCH 2/7] Fastq files don't need to be executable --- nf-customize/data/gut_1.fastq.gz | Bin nf-customize/data/gut_2.fastq.gz | Bin nf-customize/data/liver_1.fastq.gz | Bin nf-customize/data/liver_2.fastq.gz | Bin nf-customize/data/lung_1.fastq.gz | Bin nf-customize/data/lung_2.fastq.gz | Bin nf-training/data/ggal/gut_1.fq | 0 nf-training/data/ggal/gut_2.fq | 0 nf-training/data/ggal/liver_1.fq | 0 nf-training/data/ggal/liver_2.fq | 0 nf-training/data/ggal/lung_1.fq | 0 nf-training/data/ggal/lung_2.fq | 0 ...0101_I315_FC816RLABXX_L1_HUMrutRGXDIAAPE_1.fq.gz | Bin ...0101_I315_FC816RLABXX_L1_HUMrutRGXDIAAPE_2.fq.gz | Bin ...0105_I186_FC812MWABXX_L8_HUMrutRGVDIABPE_1.fq.gz | Bin ...0105_I186_FC812MWABXX_L8_HUMrutRGVDIABPE_2.fq.gz | Bin ...0121_I288_FC81DE8ABXX_L3_HUMrutRGXDIAAPE_1.fq.gz | Bin ...0121_I288_FC81DE8ABXX_L3_HUMrutRGXDIAAPE_2.fq.gz | Bin ...0122_I329_FC81DB5ABXX_L6_HUMrutRGVDIAAPE_1.fq.gz | Bin ...0122_I329_FC81DB5ABXX_L6_HUMrutRGVDIAAPE_2.fq.gz | Bin ...0128_I481_FC819P0ABXX_L5_HUMrutRGWDIAAPE_1.fq.gz | Bin ...0128_I481_FC819P0ABXX_L5_HUMrutRGWDIAAPE_2.fq.gz | Bin nf-training/data/reads/sample.fq.gz | Bin 23 files changed, 0 insertions(+), 0 deletions(-) mode change 100755 => 100644 nf-customize/data/gut_1.fastq.gz mode change 100755 => 100644 nf-customize/data/gut_2.fastq.gz mode change 100755 => 100644 nf-customize/data/liver_1.fastq.gz mode change 100755 => 100644 nf-customize/data/liver_2.fastq.gz mode change 100755 => 100644 nf-customize/data/lung_1.fastq.gz mode change 100755 => 100644 nf-customize/data/lung_2.fastq.gz mode change 100755 => 100644 nf-training/data/ggal/gut_1.fq mode change 100755 => 100644 nf-training/data/ggal/gut_2.fq mode change 100755 => 100644 nf-training/data/ggal/liver_1.fq mode change 100755 => 100644 nf-training/data/ggal/liver_2.fq mode change 100755 => 100644 nf-training/data/ggal/lung_1.fq mode change 100755 => 100644 nf-training/data/ggal/lung_2.fq mode change 100755 => 100644 nf-training/data/reads/110101_I315_FC816RLABXX_L1_HUMrutRGXDIAAPE_1.fq.gz mode change 100755 => 100644 nf-training/data/reads/110101_I315_FC816RLABXX_L1_HUMrutRGXDIAAPE_2.fq.gz mode change 100755 => 100644 nf-training/data/reads/110105_I186_FC812MWABXX_L8_HUMrutRGVDIABPE_1.fq.gz mode change 100755 => 100644 nf-training/data/reads/110105_I186_FC812MWABXX_L8_HUMrutRGVDIABPE_2.fq.gz mode change 100755 => 100644 nf-training/data/reads/110121_I288_FC81DE8ABXX_L3_HUMrutRGXDIAAPE_1.fq.gz mode change 100755 => 100644 nf-training/data/reads/110121_I288_FC81DE8ABXX_L3_HUMrutRGXDIAAPE_2.fq.gz mode change 100755 => 100644 nf-training/data/reads/110122_I329_FC81DB5ABXX_L6_HUMrutRGVDIAAPE_1.fq.gz mode change 100755 => 100644 nf-training/data/reads/110122_I329_FC81DB5ABXX_L6_HUMrutRGVDIAAPE_2.fq.gz mode change 100755 => 100644 nf-training/data/reads/110128_I481_FC819P0ABXX_L5_HUMrutRGWDIAAPE_1.fq.gz mode change 100755 => 100644 nf-training/data/reads/110128_I481_FC819P0ABXX_L5_HUMrutRGWDIAAPE_2.fq.gz mode change 100755 => 100644 nf-training/data/reads/sample.fq.gz diff --git a/nf-customize/data/gut_1.fastq.gz b/nf-customize/data/gut_1.fastq.gz old mode 100755 new mode 100644 diff --git a/nf-customize/data/gut_2.fastq.gz b/nf-customize/data/gut_2.fastq.gz old mode 100755 new mode 100644 diff --git a/nf-customize/data/liver_1.fastq.gz b/nf-customize/data/liver_1.fastq.gz old mode 100755 new mode 100644 diff --git a/nf-customize/data/liver_2.fastq.gz b/nf-customize/data/liver_2.fastq.gz old mode 100755 new mode 100644 diff --git a/nf-customize/data/lung_1.fastq.gz b/nf-customize/data/lung_1.fastq.gz old mode 100755 new mode 100644 diff --git a/nf-customize/data/lung_2.fastq.gz b/nf-customize/data/lung_2.fastq.gz old mode 100755 new mode 100644 diff --git a/nf-training/data/ggal/gut_1.fq b/nf-training/data/ggal/gut_1.fq old mode 100755 new mode 100644 diff --git a/nf-training/data/ggal/gut_2.fq b/nf-training/data/ggal/gut_2.fq old mode 100755 new mode 100644 diff --git a/nf-training/data/ggal/liver_1.fq b/nf-training/data/ggal/liver_1.fq old mode 100755 new mode 100644 diff --git a/nf-training/data/ggal/liver_2.fq b/nf-training/data/ggal/liver_2.fq old mode 100755 new mode 100644 diff --git a/nf-training/data/ggal/lung_1.fq b/nf-training/data/ggal/lung_1.fq old mode 100755 new mode 100644 diff --git a/nf-training/data/ggal/lung_2.fq b/nf-training/data/ggal/lung_2.fq old mode 100755 new mode 100644 diff --git a/nf-training/data/reads/110101_I315_FC816RLABXX_L1_HUMrutRGXDIAAPE_1.fq.gz b/nf-training/data/reads/110101_I315_FC816RLABXX_L1_HUMrutRGXDIAAPE_1.fq.gz old mode 100755 new mode 100644 diff --git a/nf-training/data/reads/110101_I315_FC816RLABXX_L1_HUMrutRGXDIAAPE_2.fq.gz b/nf-training/data/reads/110101_I315_FC816RLABXX_L1_HUMrutRGXDIAAPE_2.fq.gz old mode 100755 new mode 100644 diff --git a/nf-training/data/reads/110105_I186_FC812MWABXX_L8_HUMrutRGVDIABPE_1.fq.gz b/nf-training/data/reads/110105_I186_FC812MWABXX_L8_HUMrutRGVDIABPE_1.fq.gz old mode 100755 new mode 100644 diff --git a/nf-training/data/reads/110105_I186_FC812MWABXX_L8_HUMrutRGVDIABPE_2.fq.gz b/nf-training/data/reads/110105_I186_FC812MWABXX_L8_HUMrutRGVDIABPE_2.fq.gz old mode 100755 new mode 100644 diff --git a/nf-training/data/reads/110121_I288_FC81DE8ABXX_L3_HUMrutRGXDIAAPE_1.fq.gz b/nf-training/data/reads/110121_I288_FC81DE8ABXX_L3_HUMrutRGXDIAAPE_1.fq.gz old mode 100755 new mode 100644 diff --git a/nf-training/data/reads/110121_I288_FC81DE8ABXX_L3_HUMrutRGXDIAAPE_2.fq.gz b/nf-training/data/reads/110121_I288_FC81DE8ABXX_L3_HUMrutRGXDIAAPE_2.fq.gz old mode 100755 new mode 100644 diff --git a/nf-training/data/reads/110122_I329_FC81DB5ABXX_L6_HUMrutRGVDIAAPE_1.fq.gz b/nf-training/data/reads/110122_I329_FC81DB5ABXX_L6_HUMrutRGVDIAAPE_1.fq.gz old mode 100755 new mode 100644 diff --git a/nf-training/data/reads/110122_I329_FC81DB5ABXX_L6_HUMrutRGVDIAAPE_2.fq.gz b/nf-training/data/reads/110122_I329_FC81DB5ABXX_L6_HUMrutRGVDIAAPE_2.fq.gz old mode 100755 new mode 100644 diff --git a/nf-training/data/reads/110128_I481_FC819P0ABXX_L5_HUMrutRGWDIAAPE_1.fq.gz b/nf-training/data/reads/110128_I481_FC819P0ABXX_L5_HUMrutRGWDIAAPE_1.fq.gz old mode 100755 new mode 100644 diff --git a/nf-training/data/reads/110128_I481_FC819P0ABXX_L5_HUMrutRGWDIAAPE_2.fq.gz b/nf-training/data/reads/110128_I481_FC819P0ABXX_L5_HUMrutRGWDIAAPE_2.fq.gz old mode 100755 new mode 100644 diff --git a/nf-training/data/reads/sample.fq.gz b/nf-training/data/reads/sample.fq.gz old mode 100755 new mode 100644 From e131960c113bc1447fc82082f911b6b27208a9cf Mon Sep 17 00:00:00 2001 From: Robert Syme Date: Sun, 17 Nov 2024 21:21:04 +0000 Subject: [PATCH 3/7] Remove executable permissions from "advanced" chapter --- nf-training-advanced/groovy/main.nf | 0 nf-training-advanced/metadata/main.nf | 0 nf-training-advanced/operators/main.nf | 0 nf-training-advanced/structure/main.nf | 0 4 files changed, 0 insertions(+), 0 deletions(-) mode change 100755 => 100644 nf-training-advanced/groovy/main.nf mode change 100755 => 100644 nf-training-advanced/metadata/main.nf mode change 100755 => 100644 nf-training-advanced/operators/main.nf mode change 100755 => 100644 nf-training-advanced/structure/main.nf diff --git a/nf-training-advanced/groovy/main.nf b/nf-training-advanced/groovy/main.nf old mode 100755 new mode 100644 diff --git a/nf-training-advanced/metadata/main.nf b/nf-training-advanced/metadata/main.nf old mode 100755 new mode 100644 diff --git a/nf-training-advanced/operators/main.nf b/nf-training-advanced/operators/main.nf old mode 100755 new mode 100644 diff --git a/nf-training-advanced/structure/main.nf b/nf-training-advanced/structure/main.nf old mode 100755 new mode 100644 From f059888c60a766e6309e92a00dba8786209b06a2 Mon Sep 17 00:00:00 2001 From: Robert Syme Date: Sun, 17 Nov 2024 21:22:26 +0000 Subject: [PATCH 4/7] Fasta file doesn't need to be executable --- nf-training/data/ggal/transcriptome.fa | 0 1 file changed, 0 insertions(+), 0 deletions(-) mode change 100755 => 100644 nf-training/data/ggal/transcriptome.fa diff --git a/nf-training/data/ggal/transcriptome.fa b/nf-training/data/ggal/transcriptome.fa old mode 100755 new mode 100644 From 81d2f239200ffdd0ee70bf942bf8509b1cff9a14 Mon Sep 17 00:00:00 2001 From: Robert Syme Date: Sun, 17 Nov 2024 21:22:39 +0000 Subject: [PATCH 5/7] Configuration files don't need to be executable --- nf-training/nextflow.config | 0 1 file changed, 0 insertions(+), 0 deletions(-) mode change 100755 => 100644 nf-training/nextflow.config diff --git a/nf-training/nextflow.config b/nf-training/nextflow.config old mode 100755 new mode 100644 From 3161208f084b4a0b66072a909895121bf1996285 Mon Sep 17 00:00:00 2001 From: Robert Syme Date: Sun, 17 Nov 2024 21:22:59 +0000 Subject: [PATCH 6/7] Nextflow files don't need to be executable --- nf-training/script1.nf | 0 nf-training/script2.nf | 0 nf-training/script3.nf | 0 nf-training/script4.nf | 0 nf-training/script5.nf | 0 nf-training/script6.nf | 0 nf-training/script7.nf | 0 nf-training/snippet.nf | 0 8 files changed, 0 insertions(+), 0 deletions(-) mode change 100755 => 100644 nf-training/script1.nf mode change 100755 => 100644 nf-training/script2.nf mode change 100755 => 100644 nf-training/script3.nf mode change 100755 => 100644 nf-training/script4.nf mode change 100755 => 100644 nf-training/script5.nf mode change 100755 => 100644 nf-training/script6.nf mode change 100755 => 100644 nf-training/script7.nf mode change 100755 => 100644 nf-training/snippet.nf diff --git a/nf-training/script1.nf b/nf-training/script1.nf old mode 100755 new mode 100644 diff --git a/nf-training/script2.nf b/nf-training/script2.nf old mode 100755 new mode 100644 diff --git a/nf-training/script3.nf b/nf-training/script3.nf old mode 100755 new mode 100644 diff --git a/nf-training/script4.nf b/nf-training/script4.nf old mode 100755 new mode 100644 diff --git a/nf-training/script5.nf b/nf-training/script5.nf old mode 100755 new mode 100644 diff --git a/nf-training/script6.nf b/nf-training/script6.nf old mode 100755 new mode 100644 diff --git a/nf-training/script7.nf b/nf-training/script7.nf old mode 100755 new mode 100644 diff --git a/nf-training/snippet.nf b/nf-training/snippet.nf old mode 100755 new mode 100644 From 19c739fa57343901dca9af0eac8ff3dd90202a99 Mon Sep 17 00:00:00 2001 From: Robert Syme Date: Sun, 17 Nov 2024 21:26:54 +0000 Subject: [PATCH 7/7] Nextflow scripts don't need to be executable --- troubleshoot/exercise1/hello-gatk.nf | 0 troubleshoot/exercise2/hello-gatk.nf | 0 troubleshoot/exercise3/hello-gatk.nf | 0 troubleshoot/exercise4/hello-gatk.nf | 0 troubleshoot/exercise5/hello-gatk.nf | 0 troubleshoot/exercise6/hello-gatk.nf | 0 troubleshoot/hello-gatk.nf | 0 7 files changed, 0 insertions(+), 0 deletions(-) mode change 100755 => 100644 troubleshoot/exercise1/hello-gatk.nf mode change 100755 => 100644 troubleshoot/exercise2/hello-gatk.nf mode change 100755 => 100644 troubleshoot/exercise3/hello-gatk.nf mode change 100755 => 100644 troubleshoot/exercise4/hello-gatk.nf mode change 100755 => 100644 troubleshoot/exercise5/hello-gatk.nf mode change 100755 => 100644 troubleshoot/exercise6/hello-gatk.nf mode change 100755 => 100644 troubleshoot/hello-gatk.nf diff --git a/troubleshoot/exercise1/hello-gatk.nf b/troubleshoot/exercise1/hello-gatk.nf old mode 100755 new mode 100644 diff --git a/troubleshoot/exercise2/hello-gatk.nf b/troubleshoot/exercise2/hello-gatk.nf old mode 100755 new mode 100644 diff --git a/troubleshoot/exercise3/hello-gatk.nf b/troubleshoot/exercise3/hello-gatk.nf old mode 100755 new mode 100644 diff --git a/troubleshoot/exercise4/hello-gatk.nf b/troubleshoot/exercise4/hello-gatk.nf old mode 100755 new mode 100644 diff --git a/troubleshoot/exercise5/hello-gatk.nf b/troubleshoot/exercise5/hello-gatk.nf old mode 100755 new mode 100644 diff --git a/troubleshoot/exercise6/hello-gatk.nf b/troubleshoot/exercise6/hello-gatk.nf old mode 100755 new mode 100644 diff --git a/troubleshoot/hello-gatk.nf b/troubleshoot/hello-gatk.nf old mode 100755 new mode 100644