pekrau / samplesheet Goto Github PK

Just a network glitch or something related to recent reconfigurations?

Command '['scp', '-i', '/home/per.kraulis/samplesheet/.ssh/id_rsa', '/var/local/samplesheet/tmp/D0BD5ACXX.csv', 'hiseq@cbg:/home/hiseq.hiseq/samplesheets_illumina/2012']' returned non-zero exit status 1

In case a sample has no index, it would be good if the index sequence written to the samplesheet could be an empty string instead of 'QQQQQQ'

When the samplesheet generator duplicates the project name from "Description" to "SampleProject", only the value from the first row is used to populate all of the subsequent rows, rather than copy row-by-row.

Example output:

"FCID","Lane","SampleID","SampleRef","Index","Description","Control","Recipe","Operator","SampleProject"
"C0C0HACXX",1,"FMP_5_index4","unknown","TGACCA","D.Klevebring_11_04","N","R1","BA","D.Klevebring_11_04"
"C0C0HACXX",2,"FMP_6_index12","unknown","CTTGTA","D.Klevebring_11_04","N","R1","Ba","D.Klevebring_11_04"
"C0C0HACXX",3,"FMP_7_index4","unknown","TGACCA","D.Klevebring_11_04","N","R1","BA","D.Klevebring_11_04"
"C0C0HACXX",4,"FMP_8_index12","unknown","CTTGTA","D.Klevebring_11_04","N","R1","BA","D.Klevebring_11_04"
"C0C0HACXX",5,"FMP_9_index4","unknown","TGACCA","D.Klevebring_11_04","N","R1","BA","D.Klevebring_11_04"
"C0C0HACXX",6,"JH1_index1","unknown","ATCACG","J.Hasmats_11_02","N","R1","BA","D.Klevebring_11_04"
"C0C0HACXX",6,"JH3_index3","unknown","TTAGGC","J.Hasmats_11_02","N","R1","BA","D.Klevebring_11_04"
"C0C0HACXX",6,"JH4_index4","unknown","TGACCA","J.Hasmats_11_02","N","R1","BA","D.Klevebring_11_04"
"C0C0HACXX",6,"JH5_index5","unknown","ACAGTG","J.Hasmats_11_02","N","R1","BA","D.Klevebring_11_04"
"C0C0HACXX",6,"JH6_index6","unknown","GCCAAT","J.Hasmats_11_02","N","R1","BA","D.Klevebring_11_04"
"C0C0HACXX",6,"19_index7","unknown","CAGATC","J.Hasmats_11_03","N","R1","BA","D.Klevebring_11_04"
"C0C0HACXX",6,"20_index8","unknown","ACTTGA","J.Hasmats_11_03","N","R1","BA","D.Klevebring_11_04"
"C0C0HACXX",6,"21_index9","unknown","GATCAG","J.Hasmats_11_03","N","R1","BA","D.Klevebring_11_04"
"C0C0HACXX",6,"10_index10","unknown","TAGCTT","J.Hasmats_11_03","N","R1","BA","D.Klevebring_11_04"
"C0C0HACXX",6,"11_index11","unknown","GGCTAC","J.Hasmats_11_03","N","R1","BA","D.Klevebring_11_04"
"C0C0HACXX",7,"MPX_10_index1","unknown","ATCACG","J.Lindberg_11_09","N","R1","BA","D.Klevebring_11_04"
"C0C0HACXX",7,"MPX_10_index2","unknown","CGATGT","J.Lindberg_11_09","N","R1","BA","D.Klevebring_11_04"
"C0C0HACXX",7,"MPX_10_index3","unknown","TTAGGC","J.Lindberg_11_09","N","R1","BA","D.Klevebring_11_04"
"C0C0HACXX",7,"MPX_10_index4","unknown","TGACCA","J.Lindberg_11_09","N","R1","BA","D.Klevebring_11_04"
"C0C0HACXX",8,"miRNA-001_index1","unknown","ATCACG","N.Schoof_11_01","N","R1","BA","D.Klevebring_11_04"

The lab has expressed a wish to have the common names for species listed in the samplesheet generator genome build dropdown.
E.g. Human (hg19), Mouse (mm9) etc.

Vi pratade lite snabbt i fredags om samplesheet generatorn. Jag undrar om det är möjligt utan alltför mycket jobb att lägga till följande saker

• När varningar för hamming distance och levainstain distance kommer upp (ursäkta stavningen!) är det då möjligt att markera bägge proverna som är berörda?

Tack på förhand!

Vänliga hälsningar
Anna Leinfelt

some minor tweaks to make samplesheets play nicely with casava:

• make it impossible to enter non-accepted characters: "?()[]/=+<>:;"',*^|&." as well as space character
• don't enclose values by quotation marks in output

Supported genomes as of today are:

(master)[kalkyl1 config]$ cat tool-data/bowtie_indices.loc 
phix    phix    phiX174 
hg18    hg18    Human (hg18)
hg19    hg19    Human (hg19)
dm3 dm3 D melangogaster (dm3)   
mm9 mm9 Mouse (mm9) 
araTha_tair9    araTha_tair9    Arabidopsis thaliana (TAIR9)    
xenTro2 xenTro2 X tropicalis (xenTro2)  
sacCer2 sacCer2 S cerevisiae (sacCer2)  
WS210   WS210   C elegans (WS210)

People in the lab would like to have some instructions on how to specify the different kinds of indexes (agilent, rna etc.), e.g. at the top of the samplesheet form.

It apparently affects downstream processing, thanks to @hussius for reporting... Not sure what breaks downstream but this should definitely be handled as an input validation.

Seems like a variable was not initiated properly, the web interface gives:

Internal error

Traceback (most recent call last):
File "/usr/local/lib/python2.6/site-packages/wireframe/application.py", line 152, in call
processors(request, response) # Not a seq: single callable
File "/home/per.kraulis/samplesheet/wsgi_application.py", line 451, in view
samplerefs = _get_sampleref_options(previous_sampleref)
File "/home/per.kraulis/samplesheet/wsgi_application.py", line 737, in _get_sampleref_options
selected = selected.lower()
AttributeError: 'NoneType' object has no attribute 'lower'

...in the drop-down list instead of "unknown".

Could even warn if two samples with barcodes with e.g. an edit distance <= 2 is in the same lane.