From 5e4c023edd9f6a82b5d152c4e52168376a120df5 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Thu, 5 Dec 2019 15:18:09 +0100
Subject: [PATCH] Start work on FastQC module files

---
 .github/workflows/test-processes.yml |  2 +-
 tools/fastqc/main.nf                 | 16 --------------
 tools/fastqc/meta.yml                | 32 ++++++++++++++++++++++++++++
 tools/fastqc/test/main.nf            |  1 +
 4 files changed, 34 insertions(+), 17 deletions(-)
 create mode 100644 tools/fastqc/meta.yml
 create mode 100644 tools/fastqc/test/main.nf

diff --git a/.github/workflows/test-processes.yml b/.github/workflows/test-processes.yml
index 5e6dc699..b9c56955 100644
--- a/.github/workflows/test-processes.yml
+++ b/.github/workflows/test-processes.yml
@@ -15,4 +15,4 @@ jobs:
 
     - name: FastQC
       path: tools/fastqc/*
-      uses: ./tools/fastqc/test-action.yml
+      run: nextflow run ./tools/fastqc/test/
diff --git a/tools/fastqc/main.nf b/tools/fastqc/main.nf
index a5e8bd7f..deb570ff 100644
--- a/tools/fastqc/main.nf
+++ b/tools/fastqc/main.nf
@@ -1,19 +1,3 @@
-/*
-* Description:
-*     Run FastQC on sequenced reads
-* Keywords:
-*     read qc
-*     adapter
-* Tools:
-*     FastQC:
-*         homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
-*         documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/
-*         description: FastQC gives general quality metrics about your reads.
-*                      It provides information about the quality score distribution
-*                      across your reads, the per base sequence content (%A/C/G/T).
-*                      You get information about adapter contamination and other
-*                      overrepresented sequences.
-*/
 process fastqc {
     tag "$sample_id"
     publishDir "${params.outdir}/fastqc", mode: 'copy',
diff --git a/tools/fastqc/meta.yml b/tools/fastqc/meta.yml
new file mode 100644
index 00000000..ddd0ae7f
--- /dev/null
+++ b/tools/fastqc/meta.yml
@@ -0,0 +1,32 @@
+name: FastQC
+description: Run FastQC on sequenced reads
+keywords:
+    - Quality Control
+    - QC
+    - Adapters
+tools:
+    - fastqc:
+        description: |
+            FastQC gives general quality metrics about your reads.
+            It provides information about the quality score distribution
+            across your reads, the per base sequence content (%A/C/G/T).
+            You get information about adapter contamination and other
+            overrepresented sequences.
+        homepage: hhttps://www.bioinformatics.babraham.ac.uk/projects/fastqc/
+        documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/
+input:
+    -
+        - sample_id:
+            type: string
+            description: Sample identifier
+        - reads:
+            type: file
+            description: Input FastQ file, or pair of files
+output:
+    -
+        - report:
+            type: file
+            description: FastQC report
+            pattern: *_fastqc.{zip,html}
+authors:
+    - @ewels
diff --git a/tools/fastqc/test/main.nf b/tools/fastqc/test/main.nf
new file mode 100644
index 00000000..33242101
--- /dev/null
+++ b/tools/fastqc/test/main.nf
@@ -0,0 +1 @@
+/* A mini pipeline to test FastQC here */