From 9587f826ea08544f864d04024f546dfef3ae8454 Mon Sep 17 00:00:00 2001
From: Delphine Lariviere <lariviere.delphine@gmail.com>
Date: Fri, 14 Feb 2025 08:59:38 -0500
Subject: [PATCH] add second test

---
 ...map-for-assembly-manual-curation-tests.yml | 66 +++++++++++++++++++
 1 file changed, 66 insertions(+)

diff --git a/workflows/VGP-assembly-v2/hi-c-contact-map-for-assembly-manual-curation/hi-c-map-for-assembly-manual-curation-tests.yml b/workflows/VGP-assembly-v2/hi-c-contact-map-for-assembly-manual-curation/hi-c-map-for-assembly-manual-curation-tests.yml
index 32a298307..224a2c84a 100644
--- a/workflows/VGP-assembly-v2/hi-c-contact-map-for-assembly-manual-curation/hi-c-map-for-assembly-manual-curation-tests.yml
+++ b/workflows/VGP-assembly-v2/hi-c-contact-map-for-assembly-manual-curation/hi-c-map-for-assembly-manual-curation-tests.yml
@@ -71,3 +71,69 @@
         has_size:
           value : 1700000
           delta: 500000
+- doc: Test outline for hi-c-map-for-assembly-manual-curation.ga 2
+  job:
+    Haplotype 1:
+      class: File
+      location: https://zenodo.org/records/14230702/files/Haplotype%201.fasta
+      filetype: fasta
+    Haplotype 2:
+      class: File
+      location: https://zenodo.org/records/14230702/files/Haplotype%201.fasta
+      filetype: fasta
+    Hi-C reads:
+      class: Collection
+      collection_type: list:paired
+      elements:
+        - class: Collection
+          type: paired
+          identifier: Hi-C reads
+          elements:
+          - identifier: forward
+            class: File
+            path: https://zenodo.org/records/14230702/files/HiC%20forward.fastqsanger.gz
+          - identifier: reverse
+            class: File
+            path: https://zenodo.org/records/14230702/files/HiC%20reverse.fastqsanger.gz
+    PacBio reads:
+      class: Collection
+      collection_type: list
+      elements:
+      - class: File
+        identifier: PacBio reads.fastq.gz
+        location: https://zenodo.org/records/14230702/files/PacBio%20reads.fastq.gz
+    Do you want to add suffixes to the scaffold names?: true
+    Will you use a second haplotype?: false
+    First Haplotype suffix: H1
+    Second Haplotype suffix: H2
+    Do you want to trim the Hi-C data?: true
+    Telomere repeat to suit species: CCCTAA
+  outputs:
+    Assembly for curation:
+      asserts:
+        has_text:
+          text: ">scaffold_10.H1"
+    Gaps Bed:
+      asserts:
+        has_text:
+          text: "scaffold_10.H1	34145604	34145804"
+    Gaps Bedgraph:
+      asserts:
+        has_text:
+          text: "scaffold_10.H1	34145604	34145804	200"
+    BigWig Coverage:
+      asserts:
+        has_size:
+          value : 100000
+          delta: 40000
+    Merged Hi-C Alignments:
+      asserts:
+        has_size:
+          value : 400000000
+          delta: 50000000
+    Pretext All tracks:
+      asserts:
+        has_size:
+          value : 1600000
+          delta: 500000
+