From 011524dd31bbc23e6964d742b71e0e229f545127 Mon Sep 17 00:00:00 2001
From: LaraFuhrmann <55209716+LaraFuhrmann@users.noreply.github.com>
Date: Wed, 8 May 2024 11:30:30 +0200
Subject: [PATCH] [add virus config] config + resources for h3n2 ha segement -
 thx anika

---
 config/h3n2_ha.yaml                 | 75 +++++++++++++++++++++++++++++
 resources/h3n2_ha/gffs/h3n2_ha.gff3 |  5 ++
 resources/h3n2_ha/h3n2_ha.fasta     | 23 +++++++++
 3 files changed, 103 insertions(+)
 create mode 100644 config/h3n2_ha.yaml
 create mode 100644 resources/h3n2_ha/gffs/h3n2_ha.gff3
 create mode 100644 resources/h3n2_ha/h3n2_ha.fasta

diff --git a/config/h3n2_ha.yaml b/config/h3n2_ha.yaml
new file mode 100644
index 00000000..5ac13ede
--- /dev/null
+++ b/config/h3n2_ha.yaml
@@ -0,0 +1,75 @@
+# config-file used for the analysis of H3N2 segment HA
+# config file was used to analysis data from SRA available
+# through the SRA Run accession: SRP385331
+
+general:
+    aligner: bwa
+    primers_trimmer: samtools
+    threads: 6
+    snv_caller: lofreq
+    temp_prefix: ./temp
+    preprocessor: skip
+
+input:
+    datadir: samples/
+    samples_file: samples.tsv
+    reference: "{VPIPE_BASEDIR}/../resources/h3n2_ha/h3n2_ha.fasta"
+    genes_gff: "{VPIPE_BASEDIR}/../resources/h3n2_ha/gffs/h3n2_ha.gff3"
+    paired: true
+    read_length: 151
+
+output:
+    datadir: results/
+    snv: True
+    local: True
+    global: False
+    visualization: False
+    QA: False
+    diversity: False
+
+gunzip:
+    mem: 100000
+
+extract:
+    mem: 100000
+
+preprocessing:
+    mem: 10000
+
+sam2bam:
+    mem: 5000
+
+ref_bwa_index:
+    mem: 65536
+
+bwa_align:
+    mem: 40690
+    threads: 8
+
+bowtie_align:
+    mem: 12288
+    threads: 6
+
+coverage:
+    mem: 131072
+    threads: 32
+    time: 60
+
+minor_variants:
+    mem: 16384
+    threads: 64
+
+coverage_intervals:
+    coverage: 0
+    mem: 2000
+    threads: 1
+
+lofreq:
+    consensus: false
+
+snv:
+    consensus: false
+    localscratch: $TMPDIR
+    time: 240
+    mem: 1024
+    threads: 64
diff --git a/resources/h3n2_ha/gffs/h3n2_ha.gff3 b/resources/h3n2_ha/gffs/h3n2_ha.gff3
new file mode 100644
index 00000000..3cd57f2a
--- /dev/null
+++ b/resources/h3n2_ha/gffs/h3n2_ha.gff3
@@ -0,0 +1,5 @@
+##gff-version 3
+##sequence-region EPI1857216 1 1718
+EPI1857216  feature gene    1   48  .   +   .   gene_name="SigPep"
+EPI1857216  feature gene    49  1035    .   +   .   gene_name="HA1"
+EPI1857216  feature gene    1036    1698    .   +   .   gene_name="HA2"
diff --git a/resources/h3n2_ha/h3n2_ha.fasta b/resources/h3n2_ha/h3n2_ha.fasta
new file mode 100644
index 00000000..427694bc
--- /dev/null
+++ b/resources/h3n2_ha/h3n2_ha.fasta
@@ -0,0 +1,23 @@
+>EPI_ISL_1563628 | A/Darwin/6/2021 | A / H3N2 |  | 2021-03-16
+ATGAAGACTATCATTGCTTTGAGCAACATTCTATGTCTTGTTTTCGCTCAAAAAATACCTGGAAATGACAATAGCACGGC
+AACGCTGTGCCTTGGGCACCATGCAGTACCAAACGGAACGATAGTGAAAACAATCACAAATGACCGAATTGAAGTTACTA
+ATGCTACTGAGTTGGTTCAGAATTCATCAATAGGTGAAATATGCGGCAGTCCTCATCAGATCCTTGATGGAGGGAACTGC
+ACACTAATAGATGCTCTATTGGGGGACCCTCAGTGTGACGGCTTTCAAAATAAGGAATGGGACCTTTTTGTTGAAAGAAG
+CAGAGCCAACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTCCCTTAGGTCACTAGTTGCCTCATCCGGCACAC
+TGGAGTTTAAAAATGAAAGCTTCAATTGGACTGGAGTCAAACAAAACGGAACAAGTTCTGCGTGCATAAGGGGATCTAGT
+AGTAGTTTTTTTAGTAGATTAAATTGGTTGACCAGCTTAAACAACATATATCCAGCACAGAACGTGACTATGCCAAACAA
+GGAACAATTTGACAAATTGTACATTTGGGGGGTTCACCACCCGGATACGGACAAGAACCAAATCTCCCTGTTTGCTCAAT
+CATCAGGAAGAATCACAGTATCTACCAAAAGAAGCCAACAAGCTGTAATCCCAAATATCGGATCTAGACCCAGAATAAGG
+GATATCCCTAGCAGAATAAGCATCTATTGGACAATAGTAAAACCGGGAGACATACTTTTGATTAACAGCACAGGGAATCT
+AATTGCTCCTAGGGGTTACTTCAAAATACGAAGTGGGAAAAGCTCAATAATGAGATCAGATGCACCCATTGGCAAATGTA
+AGTCTGAATGCATCACTCCAAATGGAAGCATTCCCAATGACAAACCGTTCCAAAATGTAAACAGGATCACATACGGGGCC
+TGTCCCAGATATGTTAAGCAAAGCACCCTGAAATTGGCAACAGGAATGCGAAATGTACCAGAGAAACAAACCAGAGGCAT
+ATTTGGCGCAATAGCGGGTTTCATAGAAAATGGATGGGAGGGAATGGTGGATGGTTGGTACGGTTTCAGGCATCAAAATT
+CTGAGGGAAGAGGACAAGCAGCAGATCTCAAAAGCACTCAAGCAGCAATCGATCAAATCAATGGGAAGCTGAATCGATTG
+ATCGGAAAAACCAACGAGAAATTCCATCAGATTGAAAAAGAATTCTCAGAAGTAGAAGGAAGAGTTCAAGACCTTGAGAA
+ATATGTTGAGGACACTAAAATAGATCTCTGGTCATACAACGCGGAGCTTCTTGTTGCCCTGGAGAACCAACATACGATTG
+ACCTAACTGACTCAGAAATGAACAAACTGTTTGAAAAAACAAAGAAGCAACTGAGGGAAAATGCTGAGGATATGGGAAAT
+GGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGATCAATAAGAAATGAAACTTATGACCACAATGTGTA
+CAGGGATGAAGCATTAAACAACCGGTTCCAGATCAAGGGAGTTGAGCTGAAGTCAGGGTACAAAGATTGGATCCTATGGA
+TTTCCTTTGCCATGTCATGTTTTTTGCTTTGTATTGCTTTGTTGGGGTTCATCATGTGGGCCTGCCAAAAGGGCAACATT
+AGATGCAACATTTGCATTTGAGTGCATTAATTAAAAAC