cagnut_bwa 0.3.2 → 0.3.3
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- checksums.yaml +4 -4
- data/lib/cagnut_bwa/check_tools.rb +1 -1
- data/lib/cagnut_bwa/functions/templates/aln.sh +4 -4
- data/lib/cagnut_bwa/functions/templates/bwa_samp_one_fastq.sh +3 -3
- data/lib/cagnut_bwa/functions/templates/bwa_samse_one_fastq.sh +1 -1
- data/lib/cagnut_bwa/functions/templates/samp.sh +3 -3
- data/lib/cagnut_bwa/version.rb +1 -1
- metadata +2 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
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1
1
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---
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2
2
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SHA1:
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3
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-
metadata.gz:
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4
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-
data.tar.gz:
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3
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+
metadata.gz: 2e4b4f7800e674673c6c89535427a3338b1be1e4
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4
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+
data.tar.gz: b01d2b22d2987f7bd637338cba42cac186b04200
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5
5
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SHA512:
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6
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-
metadata.gz:
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7
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-
data.tar.gz:
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6
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+
metadata.gz: 4f4b424a1418f8a142723ba283d0fae36eee7e2f56354e50b7a3a6610982dd15ee4770304fe852a39686e0c95eb927ec8b0aed7d97031fff8c5e7f1f0be4d0d8
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7
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+
data.tar.gz: ed764a78b7f6e845908ec97bd39134c59ac37a2de02ac3d087fe8acb6f2ab6fa8ac93ee31b3ab287fa23bd90284335919cc622f548efb3418950dac7a4fa26b3
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@@ -3,7 +3,7 @@ module CagnutBwa
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3
3
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def check_tool tools_path, refs=nil
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4
4
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super if defined?(super)
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5
5
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ver = check_bwa tools_path['bwa'], refs['ref_fasta']
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6
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-
check_bwa_index tools_path['bwa'], refs['ref_fasta'] if ver.blank?
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6
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+
check_bwa_index tools_path['bwa'], refs['ref_fasta'] if !ver.blank?
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7
7
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end
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8
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def check_bwa path, ref_path
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@@ -26,14 +26,14 @@ else
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fi
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27
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#check for correct number of sequences processed, based on fastq records
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29
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-
PROCESSED=$(tail -5 #{jobs_dir}/#{script_name}.err | grep " sequences have been processed." | grep -o -
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29
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+
PROCESSED=$(tail -5 #{jobs_dir}/#{script_name}.err | grep " sequences have been processed." | grep -o "[0-9]\+")
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30
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echo "checking stdout file: " #{jobs_dir}/#{script_name}.err
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echo "bwa processed" $PROCESSED
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33
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34
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if [[ "#{input}" =~ gz$ ]]
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35
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then
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36
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-
LINESFASTQ1=$(
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36
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+
LINESFASTQ1=$(gunzip -c "#{input}" | wc -l)
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else
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38
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# non gz files
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LINESFASTQ1=$(wc -l "#{input}" | cut -d" " -f1 )
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@@ -79,13 +79,13 @@ else
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79
79
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fi
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80
80
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81
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#check for correct number of sequences processed, based on fastq records
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82
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-
PROCESSED=$(tail -5 #{jobs_dir}/#{script_name}.err | grep " sequences have been processed." | grep -o -
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82
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+
PROCESSED=$(tail -5 #{jobs_dir}/#{script_name}.err | grep " sequences have been processed." | grep -o "[0-9]\+")
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83
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echo "checking stdout file: " #{jobs_dir}/#{script_name}.err
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echo "bwa processed" $PROCESSED
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85
85
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|
86
86
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if [[ "#{input2}" =~ gz$ ]]
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87
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then
|
88
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-
LINESFASTQ2=$(
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88
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+
LINESFASTQ2=$(gunzip -c "#{input2}" | wc -l)
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else
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90
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# non gz files
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91
91
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LINESFASTQ2=$(wc -l "#{input2}" | cut -d" " -f1 )
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@@ -26,7 +26,7 @@ else
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26
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fi
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27
27
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|
28
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#check for correct number of sequences processed, based on fastq records
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29
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-
PROCESSED=$(tail -5 #{jobs_dir}/#{script_name}.err | grep " sequences have been processed." | grep -o -
|
29
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+
PROCESSED=$(tail -5 #{jobs_dir}/#{script_name}.err | grep " sequences have been processed." | grep -o "[0-9]\+")
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30
30
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31
31
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echo "checking stdout file: " #{jobs_dir}/#{script_name}.err
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echo "bwa processed" $PROCESSED
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@@ -34,8 +34,8 @@ echo "bwa processed" $PROCESSED
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if [[ "#{seq}" =~ gz$ ]]
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then
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36
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|
37
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-
LINESFASTQ1=$(
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38
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-
LINESFASTQ2=$(
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37
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+
LINESFASTQ1=$(gunzip -c "#{seq}" | wc -l)
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38
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+
LINESFASTQ2=$(gunzip -c "#{seq2}" | wc -l)
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else
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# non gz files
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@@ -27,7 +27,7 @@ fi
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#check for correct number of sequences processed, based on fastq records
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30
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-
PROCESSED=$(tail -5 #{jobs_dir}/#{script_name}.err | grep " sequences have been processed." | grep -o -
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+
PROCESSED=$(tail -5 #{jobs_dir}/#{script_name}.err | grep " sequences have been processed." | grep -o "[0-9]\+")
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echo "checking stdout file: " #{jobs_dir}/#{script_name}.err
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echo "bwa processed" $PROCESSED
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@@ -35,15 +35,15 @@ else
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fi
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36
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#check for correct number of sequences processed, based on fastq records
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38
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-
PROCESSED=$(tail -5 #{jobs_dir}/#{script_name}.err | grep " sequences have been processed." | grep -o -
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38
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+
PROCESSED=$(tail -5 #{jobs_dir}/#{script_name}.err | grep " sequences have been processed." | grep -o "[0-9]\+")
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39
39
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40
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echo "checking stdout file: " #{jobs_dir}/#{script_name}.err
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echo "bwa processed" $PROCESSED
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if [[ "#{fastq}" =~ gz$ ]]
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then
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-
LINESFASTQ1=$(
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46
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-
LINESFASTQ2=$(
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45
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+
LINESFASTQ1=$(gunzip -c "#{fastq}" | wc -l)
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46
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+
LINESFASTQ2=$(gunzip -c "#{fastq2}" | wc -l)
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else
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# non gz files
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LINESFASTQ1=$(wc -l "#{fastq}" | cut -d" " -f1 )
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data/lib/cagnut_bwa/version.rb
CHANGED
metadata
CHANGED
@@ -1,7 +1,7 @@
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1
1
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--- !ruby/object:Gem::Specification
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2
2
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name: cagnut_bwa
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3
3
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version: !ruby/object:Gem::Version
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4
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-
version: 0.3.
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4
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+
version: 0.3.3
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5
5
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platform: ruby
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6
6
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authors:
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7
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- Shi-Gang Wang
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@@ -9,7 +9,7 @@ authors:
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9
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autorequire:
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10
10
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bindir: exe
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11
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cert_chain: []
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12
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-
date: 2016-11-
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12
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+
date: 2016-11-15 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
|
15
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name: cagnut_core
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