From 390c835f9fc47574654aa0bfd55556bf376e98f2 Mon Sep 17 00:00:00 2001
From: Sviatoslav Sidorov <sviatoslav.sidorov@crick.ac.uk>
Date: Tue, 16 Mar 2021 11:54:42 +0000
Subject: [PATCH] meta.yml init; test.yml and main.nf for printing version

---
 software/hifiasm/meta.yml       | 23 ++++++++++-------------
 tests/software/hifiasm/main.nf  | 18 +++++++++---------
 tests/software/hifiasm/test.yml | 22 +++++-----------------
 3 files changed, 24 insertions(+), 39 deletions(-)

diff --git a/software/hifiasm/meta.yml b/software/hifiasm/meta.yml
index 413aad8d..9ef62628 100644
--- a/software/hifiasm/meta.yml
+++ b/software/hifiasm/meta.yml
@@ -1,20 +1,17 @@
-name: fastqc
-description: Run FastQC on sequenced reads
+name: hifiasm
+description: Run hifiasm on Pacbio HiFi reads
 keywords:
-    - quality control
-    - qc
-    - adapters
+    - genome assembly
+    - pacbaio
+    - hifi
+    - long reads
     - fastq
 tools:
-    - fastqc:
+    - hifiasm:
         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: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
-        documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/
+            hifiasm generates a genome assembly from long Pacbio HiFi reads. ...Haplotype resolution ...Using short reads.
+        homepage: https://github.com/chhylp123/hifiasm
+        documentation: https://github.com/chhylp123/hifiasm
 params:
     - outdir:
         type: string
diff --git a/tests/software/hifiasm/main.nf b/tests/software/hifiasm/main.nf
index f10b2357..66824584 100644
--- a/tests/software/hifiasm/main.nf
+++ b/tests/software/hifiasm/main.nf
@@ -2,27 +2,27 @@
 
 nextflow.enable.dsl = 2
 
-include { FASTQC } from '../../../software/fastqc/main.nf' addParams( options: [:] )
+include { HIFIASM } from '../../../software/hifiasm/main.nf' addParams( options: [:] )
 
-/*
+/* 
  * Test with single-end data
  */
-workflow test_fastqc_single_end {
+/* workflow test_fastqc_single_end {
 
     def input = []
     input = [ [ id:'test', single_end:true ], // meta map
               [ file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_1.fastq.gz", checkIfExists: true) ] ]
     FASTQC ( input )
-}
+} */
 
 /*
- * Test with paired-end data
+ * Test version printing
  */
-workflow test_fastqc_paired_end {
+workflow test_hifiasm_version {
 
-    def input = []
+/*     def input = []
     input = [[id: 'test', single_end: false], // meta map
              [file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_1.fastq.gz", checkIfExists: true),
-              file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_2.fastq.gz", checkIfExists: true)]]
-    FASTQC (input)
+              file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_2.fastq.gz", checkIfExists: true)]] */
+    HIFIASM ()
 }
diff --git a/tests/software/hifiasm/test.yml b/tests/software/hifiasm/test.yml
index 0fe0ebe0..3825b238 100644
--- a/tests/software/hifiasm/test.yml
+++ b/tests/software/hifiasm/test.yml
@@ -1,19 +1,7 @@
-- name: fastqc single-end
-  command: nextflow run ./tests/software/fastqc/ -entry test_fastqc_single_end -c tests/config/nextflow.config
+- name: hifiasm 
+  command: nextflow run ./tests/software/hifiasm/ -entry test_hifiasm_version -c tests/config/nextflow.config
   tags:
-    - fastqc
-    - fastqc_single_end
+    - hifiasm
+    - hifiasm_version
   files:
-    - path: ./output/fastqc/test_fastqc.html
-    - path: ./output/fastqc/test_fastqc.zip
-
-- name: fastqc paired-end
-  command: nextflow run ./tests/software/fastqc/ -entry test_fastqc_paired_end -c tests/config/nextflow.config
-  tags:
-    - fastqc
-    - fastqc_paired_end
-  files:
-    - path: ./output/fastqc/test_1_fastqc.html
-    - path: ./output/fastqc/test_2_fastqc.html
-    - path: ./output/fastqc/test_2_fastqc.zip
-    - path: ./output/fastqc/test_1_fastqc.zip
+    - path: ./output/hifiasm/VERSION.txt