Building a configuration file

[liuyu988]

now I have one .bam file about 7000+ cell, and the cells have been divided into two types, i want to compare the AS event between this two types. but i got an unexpected error.

my meta.tsv:

cell_id grouping_level_1 grouping_level_2
Sper_AACCATGAGATTACCC-1 Spermatocytes-E3 Eu
Sper_AACCATGGTATCAGTC-1 Spermatocytes-E3 Para
Sper_AACTCCCGTCAGTGGA-1 Spermatocytes-E3 Eu
Sper_AAGACCTAGCGGATCA-1 Spermatocytes-E3 Eu

my .conf:

params {
dataname = "Sper"
SICILIAN = false
samplesheet = "samplesheet.csv"
annotator_pickle = "gtf_part.pkl"
exon_pickle = "gtf_part_exon_bounds.pkl"
splice_pickle = "gtf_part_splices.pkl"
gtf = "gtf_part.gtf"
meta = "meta.tsv"
pin_S = 0.1
pin_z = 0.0
bounds = 5
light = false
svd_type = "normdonor"
n_perms = 100
grouping_level_2 = "grouping_level_1"
grouping_level_1 = "grouping_level_2"
libraryType = "10X"
run_analysis = true
}

my samplesheet.csv:

Sper, cellsorted.bam

my error:

[-        ] process > NFCORE_SPLIZ:SPLIZ_PIPELINE:PREPROCESS:CONVERT_BAM:CLASS_INPUT_10X     -
[-        ] process > NFCORE_SPLIZ:SPLIZ_PIPELINE:PREPROCESS:CONVERT_BAM:PROCESS_CLASS_INPUT -
[-        ] process > NFCORE_SPLIZ:SPLIZ_PIPELINE:PREPROCESS:CONVERT_BAM:ANN_SPLICES         -
[-        ] process > NFCORE_SPLIZ:SPLIZ_PIPELINE:SPLIZ:CALC_SPLIZVD                         -
[-        ] process > NFCORE_SPLIZ:SPLIZ_PIPELINE:ANALYSIS:PVAL_PERMUTATIONS                 -
[-        ] process > NFCORE_SPLIZ:SPLIZ_PIPELINE:ANALYSIS:FIND_SPLIZ_SITES                  -
[-        ] process > NFCORE_SPLIZ:SPLIZ_PIPELINE:ANALYSIS:SUMMARIZE_RESULTS                 -
Execution cancelled -- Finishing pending tasks before exit
-[nf-core/spliz] Pipeline completed with errors-
WARN: To render the execution DAG in the required format it is required to install Graphviz -- See http://www.graphviz.org for more info.
Execution aborted due to an unexpected error
 -- Check script '/public2/home/rotation/.nextflow/assets/salzmanlab/spliz/./workflows/./../subworkflows/local/./../../modules/local/class_input_10X.nf' at line: 2 or see '.nextflow.log' file for more details

whether is my .conf wrong? i have no idea to deal with this. And for one .bam file, i don't see some tips in your pipeline, could you offer some help? thanks a lot

Yu Liu

[liuyu988]

And whether i should firstly split the big .bam file into some small .bam files by barcode ID?

[liuyu988]

And whether i should firstly split the big .bam file into some small .bam files by barcode ID?

[liuyu988]

Hi, and i want to read more details for using SpliZ,but It looks like https://nf-co.re/spliz/usage doesn't exist.

[MEFarhadieh]

Dear liuyu988, have you tried test run?
Have you checked work directory or log file?
According line 2 of class_input_10X.nf ,tag "${params.dataname}", I guess this error is due to define parameters. Maybe you have syntax problems in your config file for example you forgot to use tab space for parameters after brace.
Also, I recommend you install Graphviz.
I hope these solutions would be helpful because I'm SpliZ user (I'm not in SpliZ team).