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This repository has been archived by the owner on Feb 7, 2023. It is now read-only.
I am having an issue running this. I have altered the config.yaml (pasted below). I read an another issue that full paths were required so I added these, but have removed identifying names. (also can the pipeline take compressed fq files?). LIne 15 is the transcriptome: "/PATH/TO/analysis/GRCh38.primary_assembly.genome.fa" - line. I cant see what is wrong with this. Sorry! can you please help?
Pete
I get the following error:
pipeline-transcriptome-de]$ snakemake --use-conda -j 24 all
SyntaxError:
Input and output files have to be specified as strings or lists of strings.
File "/PATH/analysis/pipeline-transcriptome-de/Snakefile", line 15, in
File "/PATH/analysis/pipeline-transcriptome-de/snakelib/utils.snake", line 15, in
General pipeline parameters:
Name of the pipeline:
pipeline: "pipeline-transcriptome-de_phe"
ABSOLUTE path to directory holding the working directory:
In my case it appears to be a rule that's been implemented in the snakelib/utils.snake document that is preventing the pipeline from recognising the input files.
I've tried hashing out that line in the Snakefile (line 15, include: "snakelib/utils.snake"), and so far the pipeline appears to be running (now on the mapping step). Happy to discuss more, and would love to hear feedback from the ONT side on what might need to be updated.
EnJun
PS: Also replied with something similar on the ONT community forums
Dear Nanoporetech,
I am having an issue running this. I have altered the config.yaml (pasted below). I read an another issue that full paths were required so I added these, but have removed identifying names. (also can the pipeline take compressed fq files?). LIne 15 is the transcriptome: "/PATH/TO/analysis/GRCh38.primary_assembly.genome.fa" - line. I cant see what is wrong with this. Sorry! can you please help?
Pete
I get the following error:
pipeline-transcriptome-de]$ snakemake --use-conda -j 24 all
SyntaxError:
Input and output files have to be specified as strings or lists of strings.
File "/PATH/analysis/pipeline-transcriptome-de/Snakefile", line 15, in
File "/PATH/analysis/pipeline-transcriptome-de/snakelib/utils.snake", line 15, in
General pipeline parameters:
Name of the pipeline:
pipeline: "pipeline-transcriptome-de_phe"
ABSOLUTE path to directory holding the working directory:
workdir_top: "/PATH/TO/analysis/"
Results directory:
resdir: "results"
Repository URL:
repo: "https://github.com/nanoporetech/pipeline-transcriptome-de"
Pipeline-specific parameters:
Transcriptome fasta
transcriptome: "/PATH/TO/analysis/GRCh38.primary_assembly.genome.fa"
Annotation GFF/GTF
annotation: "/PATH/TO/analysis/gencode.v39.annotation.gff3"
Control samples
control_samples:
C1: "/PATH/TO/analysis/R1_.fastq.gz"
C2: "/PATH/TO/analysis/R2_.fastq.gz"
C3: "/PATH/TO/analysis/R3_.fastq.gz"
Treated samples
treated_samples:
IR1: "/PATH/TO/analysis/R4_.fastq.gz"
IR2: "/PATH/TO/analysis/R5_.fastq.gz"
IR3: "/PATH/TO/analysis/R6_.fastq.gz"
Minimap2 indexing options
minimap_index_opts: ""
Minimap2 mapping options
minimap2_opts: ""
Maximum secondary alignments
maximum_secondary: 100
Secondary score ratio (-p for minimap2)
secondary_score_ratio: 1.0
Salmon library type
salmon_libtype: "U"
Count filtering options - customize these according to your experimental design:
Genes expressed in minimum this many samples
min_samps_gene_expr: 3
Transcripts expressed in minimum this many samples
min_samps_feature_expr: 1
Minimum gene counts
min_gene_expr: 10
Minimum transcript counts
min_feature_expr: 3
Threads
threads: 24
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