Merge branch 'master' of https://github.com/conchoecia/hormiphora

annotation/Snakefile

@@ -27,8 +27,8 @@ import gzip
 MAXTHREADS  = 90
 REF      = "raw_files/UCSC_Hcal_v1.fa.gz"
 #Prefix must not have underscores or periods
-PREFIX   = "Hcv1a1d20200309"
-CSV      = "raw_files/Hcal_annotation_v68.csv"
+PREFIX   = "Hcv1a1d20200325"
+CSV      = "raw_files/Hcal_annotation_v74.csv"
 FLNC     = "raw_files/GLO64_flnc.fastq.gz"
 PILONJAR = "raw_files/pilon-1.22.jar"
 RNAF     = "raw_files/Hc1_lib17_run1_ILL_RNAseq_R1.fastq.gz"
@@ -99,8 +99,8 @@ rule gen_transcripts_from_spreadsheet:
     input:
         ref = "tempfiles/ref.fa",
         csv = CSV,
-        has = "horm_annotation_script.py",
-        tc  = "transcript_classes.py"
+        has = "scripts/horm_annotation_script.py",
+        tc  = "scripts/transcript_classes.py"
     output:
         gff = "final_output/{fix}.gff"
     shell:

annotation/make_release.sh

@@ -1,5 +1,5 @@
 #!/bin/bash
-RELEASE=Hcv1a1d20200309
+RELEASE=Hcv1a1d20200324
 mkdir ${RELEASE}_release
 find ./final_output/ -type f -name "*" -exec cp {} ${RELEASE}_release \;
 rm ${RELEASE}_release/*vcf*
@@ -36,12 +36,13 @@ mv ${RELEASE}_release/*_phased_* ${RELEASE}_release/phased/
 mv ${RELEASE}_release/*empty* ${RELEASE}_release/phased/
 mv ${RELEASE}_release/*transcripts_unique_to_h* ${RELEASE}_release/phased/
 
-
 mkdir ${RELEASE}_release/partly_phased
-mv ${RELEASE}_release/h1_*.pep ${RELEASE}_release/partly_phased/
-mv ${RELEASE}_release/h2_*.pep ${RELEASE}_release/partly_phased/
-mv ${RELEASE}_release/h1_*.fasta ${RELEASE}_release/partly_phased/
-mv ${RELEASE}_release/h2_*.fasta ${RELEASE}_release/partly_phased/
+mv ${RELEASE}_release/h1_*.pep.gz ${RELEASE}_release/partly_phased/
+mv ${RELEASE}_release/h2_*.pep.gz ${RELEASE}_release/partly_phased/
+mv ${RELEASE}_release/h1_*.fasta.gz ${RELEASE}_release/partly_phased/
+mv ${RELEASE}_release/h2_*.fasta.gz ${RELEASE}_release/partly_phased/
 
+# add the relase notes
+cat raw_files/release_template.md | sed 's/RELEASEPREFIX/${RELEASE}' > ${RELEASE}_release/README_${RELEASE}.md
 
 tar -czvf ${RELEASE}_release.tar.gz ${RELEASE}_release