From 3ec4f63fd845022e68688f8ecf7f06c4e4a8ab14 Mon Sep 17 00:00:00 2001
From: drpatelh <drhpatel@gmail.com>
Date: Wed, 5 Aug 2020 16:28:42 +0100
Subject: [PATCH 1/2] Use correct link to fastqc

---
 .github/workflows/{ => deprecated}/cutadapt.yml       | 0
 .github/workflows/{ => deprecated}/fastqc.yml         | 0
 .github/workflows/{ => deprecated}/samtools_index.yml | 0
 .github/workflows/{ => deprecated}/samtools_sort.yml  | 0
 .github/workflows/{ => deprecated}/tcoffee.yml        | 0
 .github/workflows/{ => deprecated}/trim_galore.yml    | 0
 software/fastqc/main.nf                               | 2 +-
 7 files changed, 1 insertion(+), 1 deletion(-)
 rename .github/workflows/{ => deprecated}/cutadapt.yml (100%)
 rename .github/workflows/{ => deprecated}/fastqc.yml (100%)
 rename .github/workflows/{ => deprecated}/samtools_index.yml (100%)
 rename .github/workflows/{ => deprecated}/samtools_sort.yml (100%)
 rename .github/workflows/{ => deprecated}/tcoffee.yml (100%)
 rename .github/workflows/{ => deprecated}/trim_galore.yml (100%)

diff --git a/.github/workflows/cutadapt.yml b/.github/workflows/deprecated/cutadapt.yml
similarity index 100%
rename from .github/workflows/cutadapt.yml
rename to .github/workflows/deprecated/cutadapt.yml
diff --git a/.github/workflows/fastqc.yml b/.github/workflows/deprecated/fastqc.yml
similarity index 100%
rename from .github/workflows/fastqc.yml
rename to .github/workflows/deprecated/fastqc.yml
diff --git a/.github/workflows/samtools_index.yml b/.github/workflows/deprecated/samtools_index.yml
similarity index 100%
rename from .github/workflows/samtools_index.yml
rename to .github/workflows/deprecated/samtools_index.yml
diff --git a/.github/workflows/samtools_sort.yml b/.github/workflows/deprecated/samtools_sort.yml
similarity index 100%
rename from .github/workflows/samtools_sort.yml
rename to .github/workflows/deprecated/samtools_sort.yml
diff --git a/.github/workflows/tcoffee.yml b/.github/workflows/deprecated/tcoffee.yml
similarity index 100%
rename from .github/workflows/tcoffee.yml
rename to .github/workflows/deprecated/tcoffee.yml
diff --git a/.github/workflows/trim_galore.yml b/.github/workflows/deprecated/trim_galore.yml
similarity index 100%
rename from .github/workflows/trim_galore.yml
rename to .github/workflows/deprecated/trim_galore.yml
diff --git a/software/fastqc/main.nf b/software/fastqc/main.nf
index 7f882525..ed80e019 100644
--- a/software/fastqc/main.nf
+++ b/software/fastqc/main.nf
@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName } from './lib/functions'
 
 process FASTQC {
     tag "$meta.id"

From 4a65c77e58a3de8b792ca9c8d8983e18235ae7de Mon Sep 17 00:00:00 2001
From: drpatelh <drhpatel@gmail.com>
Date: Wed, 5 Aug 2020 16:34:07 +0100
Subject: [PATCH 2/2] deprecated/trim_galore/Dockerfile

---
 deprecated/trim_galore/Dockerfile | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/deprecated/trim_galore/Dockerfile b/deprecated/trim_galore/Dockerfile
index ef13a1bf..6a66cf2c 100644
--- a/deprecated/trim_galore/Dockerfile
+++ b/deprecated/trim_galore/Dockerfile
@@ -2,6 +2,8 @@ FROM nfcore/base:1.7
 LABEL authors="phil.ewels@scilifelab.se" \
     description="Docker image for nf-core modules trimgalore"
 
+#### THIS IS  A BUG
+
 # foobar
 COPY environment.yml /
 RUN conda env create -f /environment.yml && conda clean -a