Update .gitpod.yml

.gitpod.yml

@@ -14,31 +14,6 @@ ports:
   visibility: public
 
 tasks:
-  - name: Install Singularity 3.11.4
-  # https://docs.sylabs.io/guides/3.0/user-guide/installation.html
-    init: |
-      cd /workspace/treeval-curation/
-
-      sudo apt-get update && sudo apt-get install -y \
-      build-essential \
-      libssl-dev \
-      uuid-dev \
-      libgpgme11-dev \
-      squashfs-tools \
-      libseccomp-dev \
-      pkg-config
-
-      mkdir -p $GOPATH/src/github.com/sylabs && \
-      cd $GOPATH/src/github.com/sylabs && \
-      wget https://github.com/sylabs/singularity/releases/download/v3.11.4/singularity-ce-3.11.4.tar.gz && \
-      tar -xzf singularity-ce-3.11.4.tar.gz && \
-      cd ./singularity-ce-3.11.4 && \
-      ./mconfig
-
-      ./mconfig && \
-      make -C ./builddir && \
-      sudo make -C ./builddir install
-
   - name: Install Nextflow
   # https://www.nextflow.io/docs/latest/getstarted.html
     init: |
@@ -48,7 +23,7 @@ tasks:
 
       chmod +x nextflow
 
-      nextflow self-update
+      bash nextflow self-update
 
   - name: Install JBrowse2
   # https://jbrowse.org/jb2/download/#jbrowse-cli-tools
@@ -63,19 +38,12 @@ tasks:
 
       npx serve . -l 3000
 
-  - name: Install TreeVal Pipeline
-  # https://github.com/sanger-tol/treeval
-    init: |
-      cd /workspace/treeval-curation/
-
-      git clone -b pre-tag https://github.com/sanger-tol/treeval.git
-
-  - name: Install Curtation Pretext
+  - name: Install Curation Pretext
   # https://github.com/sanger-tol/curationpretext
     init: |
       cd /workspace/treeval-curation/
 
-      git clone -b dev https://github.com/sanger-tol/curationpretext.git
+      git clone -b 1.0.0 https://github.com/sanger-tol/curationpretext.git
 
   - name: Install HiGlass
   # https://docs.higlass.io/tutorial.html
@@ -126,17 +94,6 @@ tasks:
     init: |
       gp preview https://bga23.org/treeval-curation/Tutorial/
 
-github:
-  prebuilds:
-    # enable for the master/default branch (defaults to true)
-    master: true
-    # add a "Review in Gitpod" button as a comment to pull requests (defaults to true)
-    addComment: true
-    # add a "Review in Gitpod" button to pull requests (defaults to false)
-    addBadge: true
-    # add a label once the prebuild is ready to pull requests (defaults to false)
-    addLabel: prebuilt-in-gitpod
-
 vscode:
   extensions:                               # based on nf-core.nf-core-extensionpack
     - codezombiech.gitignore                # Language support for .gitignore files

BGA-test.yaml

@@ -0,0 +1,36 @@
+assembly:
+  assem_level: scaffold
+  sample_id: Oscheius_DF5033
+  defined_class: nematode
+  assem_version: 1
+  project_id: DTOL
+reference_file: /workspace/treeval-curation/Oscheius_DF5033/genomic_data/Oscheius_DF5033.fa
+map_order: length
+assem_reads:
+  read_type: hifi
+  read_data: /workspace/treeval-curation/Oscheius_DF5033/pacbio/
+  supplementary_data: path
+hic_data:
+  hic_cram: /workspace/treeval-curation/Oscheius_DF5033/hic-arima2/
+  hic_aligner: minimap2
+alignment:
+  data_dir: /workspace/treeval-curation/gene_alignment_data/
+  geneset: "OscheiusTipulae.ASM1342590v1,CaenorhabditisElegans.WBcel235,Gae_host.Gae"
+  common_name: "not in use"
+self_comp:
+  motif_len: 0
+  mummer_chunk: 10
+intron:
+  size: "50k"
+telomere:
+  teloseq: TTAGGG
+synteny:
+  synteny_path: /workspace/treeval-curation/synteny
+  synteny_genomes: "SuperNematode"
+busco:
+  lineages_path: /workspace/treeval-curation/busco/v5
+  lineage: nematoda_odb10
+kmer_profile:
+  # kmer_length will act as input for kmer_read_cov fastk and as the name of folder in profile_dir
+  kmer_length: 31
+  dir: /workspace/treeval-curation/