From d1ebcb034a36eadfe4582df0ffb00501bf722b51 Mon Sep 17 00:00:00 2001
From: Tyghe Vallard <vallardt@gmail.com>
Date: Thu, 28 Jan 2016 15:42:57 -0500
Subject: [PATCH] Slightly working

---
 pyjip/README.md      | 46 ++++++++++++++++++++++++++++++++++++++++++++
 pyjip/bwa_index.jip  |  8 +-------
 pyjip/cutadapt.jip   | 24 ++++++++++++++++-------
 pyjip/simplepipe.jip | 11 +++++++----
 4 files changed, 71 insertions(+), 18 deletions(-)
 create mode 100644 pyjip/README.md

diff --git a/pyjip/README.md b/pyjip/README.md
new file mode 100644
index 0000000..c145d8c
--- /dev/null
+++ b/pyjip/README.md
@@ -0,0 +1,46 @@
+# Simple jip pipeline
+
+[Jip Docs](http://pyjip.readthedocs.org/en/latest)
+
+# Dirty install
+
+Would be fun later to maybe make a task to install executables inside a jip task
+using conda.
+
+For now do it manually
+```
+conda install bwa samtools cutadapt
+```
+
+# Execute pipeline
+
+For the examples/tests I ran I used the 947 sample that comes with the ngs_mapper pipeline
+
+
+## Single threaded(non-piped)
+
+```
+./simplepipe.jip -r ../../functional/947.ref.fasta -f ../../functional/947/947_S32_L001_R{1,2}_001_2013_12_17.fastq
+```
+
+### Dry run
+
+```
+./simplepipe.jip -r ../../functional/947.ref.fasta -f ../../functional/947/947_S32_L001_R{1,2}_001_2013_12_17.fastq -- --show --dry
+```
+
+## Multy threaded(named pipe)
+
+```
+jip server &
+cat <<EOF > ~/.jip/jip.json
+    {
+        "cluster": "jip.grids.JIP",
+        "jip_cluster":{
+            "port": 5556
+        }
+    }
+EOF
+
+jip submit simplepipe.jip -r ../../functional/947.ref.fasta -f ../../functional/947/947_S32_L001_R{1,2}_001_2013_12_17.fastq --pipe
+```
diff --git a/pyjip/bwa_index.jip b/pyjip/bwa_index.jip
index 1fb86e6..83d6f88 100755
--- a/pyjip/bwa_index.jip
+++ b/pyjip/bwa_index.jip
@@ -14,13 +14,7 @@ options['output'].default = "${reference}.bwt"
 #%end
 
 #%begin validate
-import os
-try:
-    os.makedirs(options['output'].get())
-except OSError as e:
-    if e.errno != 17:
-        validation_error('Failed to create "${output}": ' + str(e))
 #%end
 
-cp ${reference|abs} ${output}
+cp ${reference|abs} ${output|ext}
 bwa index ${output|ext}
diff --git a/pyjip/cutadapt.jip b/pyjip/cutadapt.jip
index df00dc0..ed73e9e 100755
--- a/pyjip/cutadapt.jip
+++ b/pyjip/cutadapt.jip
@@ -2,30 +2,40 @@
 # Runs cutadapt with only quality filter
 #
 # usage:
-#   cutadapt [-o <outsuffix>] -q <qualcutoff>... -f <fastq>...
+#   cutadapt -q <qualcutoff>... -f <fastq>... [-o <outr1>] [-p <outr2>] [--pipe]
 #
 # Options:
 #   -f, --fastq <fastq>            The input fastq file[s]
 #   -q, --qualcutoff <qualcutoff>  The quality cutoff [Default: 25]
-#   -o, --outsuffix <outsuffix>    The output suffix [Default: .cutadapt]
+#   -o, --outr1 <outr1>            R1 output fastq [Default: output_r1.cutadapt]
+#   -p, --outr2 <outr2>            R2 output fastq
+#   --pipe                         Flag to create named pipes for output [Default: False]
 
 #%begin init
-add_output('output_r1', '', short='-o')
-add_output('output_r2', '', short='-p')
+add_output('output', [options['outr1']], nargs='+')
 #%end
 
 #%begin setup
-options['output_r1'].set('output_r1' + options['outsuffix'].get())
 if len(options['fastq']) == 2:
     options['qualcutoff'].join = ','
     if len(options['qualcutoff']) != len(options['fastq']):
         qualcutoff = options['qualcutoff'].value[0]
         options['qualcutoff'].set([qualcutoff,qualcutoff])
-    options['output_r2'].set('output_r2' + options['outsuffix'].get())
+    if not options['outr2']:
+        options['outr2'].set('output_r2.cutadapt')
+    options['output'].append(options['outr2'])
 #%end
 
 #%begin validate
 assert len(options['fastq']) == len(options['qualcutoff']), validation_error('qualcuttoff must have same number of entries as fastq')
 #%end
 
-cutadapt ${output_r1|arg} ${output_r2|arg|else('')} -q ${qualcutoff} ${fastq}
+if [ "${pipe|arg}" == "--pipe" ]
+then
+    mkfifo ${outr1} ${outr2|else('')}
+fi
+cutadapt ${outr1|arg} ${outr2|arg|else('')} -q ${qualcutoff} ${fastq}
+if [ "${pipe|arg}" == "--pipe" ]
+then
+    rm ${outr1} ${outr2|else('')}
+fi
diff --git a/pyjip/simplepipe.jip b/pyjip/simplepipe.jip
index 764acaa..4bd20b1 100755
--- a/pyjip/simplepipe.jip
+++ b/pyjip/simplepipe.jip
@@ -3,7 +3,7 @@
 # Simple pipeline to run cutadapt, bwa index, bwa mem, samtools view
 #
 # Usage:
-#   simplepipe -r <reference> -f <fastq>... [-q <qualcutoff>...] [-o <output>]
+#   simplepipe -r <reference> -f <fastq>... [-q <qualcutoff>...] [-o <output>] [--pipe]
 #
 # Options:
 #   -r, --reference <reference>       Reference file to index and map to
@@ -12,11 +12,14 @@
 #                                     [Default: 25]
 #   -o, --output <output>             The output bam file
 #                                     [Default: mapped.bam]
+#   -p, --pipe                        To use named pipe(have to submit jip job for this to work)
+#                                     [Default: False]
 
 #%begin pipeline
-trimmed = run('cutadapt', fastq=options['fastq'], qualcutoff=options['qualcutoff'])
+trimmed = run('cutadapt', fastq=options['fastq'], qualcutoff=options['qualcutoff'], pipe=options['pipe'])
 index_ref = run('bwa_index', reference=options['reference'])
-sam = run('bwa_mem', reference=reference, fastq=[trimmed.output_r1, trimmed.output_r2])
+sam = run('bwa_mem', reference=reference, fastq=['output_r1.cutadapt', 'output_r2.cutadapt'])
 bam = run('sam_to_bam', input=sam, output=options['output'])
-index_ref >> sam
+
+index_ref >> (sam | bam)
 #%end