.snakemake/scripts folder is empty

[MarleyCodes]

The pipeline does not seem to create the tmp files of the scripts within the batch/.snakemake/scripts directory. Which results in the crash of the following command:

source /home/mye/miniconda2/bin/activate '/data/sag/2019/MYE_18020068_2019_SingleCellTomBras/dropSeqPipe/batch1/.snakemake/conda/f854f536'; set -euo pipefail; Rscript --vanilla /data/sag/2019/MYE_18020068_2019_SingleCellTomBras/dropSeqPipe/batch1/.snakemake/scripts/tmp5wipn0w_.plot_violine.R'

With error:

Fatal error: cannot open file '/data/sag/2019/MYE_18020068_2019_SingleCellTomBras/dropSeqPipe/batch1/.snakemake/scripts/tmp5wipn0w_.plot_violine.R': No such file or directory

Is something going wrong with rights or directories? Any clues would be greatly appreciated.

config.yaml:

CONTACT:
  email: ''
  person: ''
LOCAL:
    temp-directory: /data/sag/2019/MYE_18020068_2019_SingleCellTomBras/maize/small_set/dropseqpipe/tmp
    memory: 8g
    raw_data: /data/sag/2019/MYE_18020068_2019_SingleCellTomBras/dropSeqPipe/batch1/RAW_DATA
    results: maize_results
META:
    species: 
        maize:
            build: 73
            release: 42
    ratio: 0.2
    reference-directory: /data/sag/2019/MYE_18020068_2019_SingleCellTomBras/maize
    gtf_biotypes: gtf_biotypes.yaml

FILTER:
    barcode-whitelist: ''
    5-prime-smart-adapter: AATGATACGGCGACCACCGAGATCTACACGCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC
    cell-barcode:
        start: 1
        end: 12
    UMI-barcode:
        start: 13
        end: 20
    cutadapt:
        adapters-file: NexteraPE-PE.fa
        R1:
            quality-filter: 20
            maximum-Ns: 1
            extra-params: ''
        R2:
            quality-filter: 20
            minimum-adapters-overlap: 6
            minimum-length: 15
            extra-params: ''
MAPPING:
    STAR:
        genomeChrBinNbits: 18
        outFilterMismatchNmax: 10
        outFilterMismatchNoverLmax: 0.3
        outFilterMismatchNoverReadLmax: 1
        outFilterMatchNmin: 0
        outFilterMatchNminOverLread: 0.66
        outFilterScoreMinOverLread: 0.66
EXTRACTION:
    LOCUS:
        - CODING
        - UTR
    strand-strategy: SENSE
    UMI-edit-distance: 1
    minimum-counts-per-UMI: 0

[caramirezal]

Could you please provide an already to use example to run for testing with a fully filled yaml template example? It would be very helpful. I'm having the following issue. It's weird because I'm pretty sure that the fastq.gz files are there but the message say they aren't. I even use the full path.

SystemExit:     No sample files found in the ~/sc/dropSeqPipe/data/fastq_slides/ directory.
        Please check that the path for the raw data is set properly in config.yaml

This is the whole config.yaml file.

CONTACT:
  email: 
  person: 
LOCAL:
    temp-directory: .tmp
    memory: 4g
    raw_data: ~/sc/dropSeqPipe/data/fastq_slides/
    results: results
META:
    species:
        mus_musculus:
            build: 38
            release: 1
    ratio: 0.2
    reference-directory: ref
    gtf_biotypes: gtf_biotypes.yaml
FILTER:
    barcode-whitelist: ''
    5-prime-smart-adapter: ''
    cell-barcode:
        start: 1
        end: 12
    UMI-barcode:
        start: 13
        end: 21
    cutadapt:
        adapters-file: NexteraPE-PE.fa
        R1:
            quality-filter: 20
            maximum-Ns: 1
            extra-params: ''
        R2:
            quality-filter: 20
            minimum-adapters-overlap: 6
            minimum-length: 15
            extra-params: ''
MAPPING:
    STAR:
        genomeChrBinNbits: 18
        outFilterMismatchNmax: 10
        outFilterMismatchNoverLmax: 0.3
        outFilterMismatchNoverReadLmax: 1
        outFilterMatchNmin: 0
        outFilterMatchNminOverLread: 0.66
        outFilterScoreMinOverLread: 0.66
EXTRACTION:
    LOCUS:
        - CODING
        - UTR
    strand-strategy: SENSE
    UMI-edit-distance: 1
    minimum-counts-per-UMI: 0
DEBUG: False

Again a complete example would be great, maybe with a tiny number of fastq sequences to be able to run easily. Thanks for the tool ;).

[Hoohm]

Hello @caramirezal I would not use relative paths at all. We sometimes get odd behaviors with those. There is a test data in the .test folder. You can download this by using this command: git submodule update --init

[vuzun]

Hi,

I'm having the same issue as @caramirezal I have .fastq.gz files in the data folder, but I still get the "no samples found" error. I tried the full paths in both the snakemake call and the yaml, but to no success.

I extracted the pipeline from the 0.4 tar.gz archive.

Any suggestions?

Thanks!