Pipeline to fetch metadata and raw FastQ files from public databases
--download_method ftp
) but you can choose to use sra-tools or Aspera using --download_method sratools
or --download_method aspera
, respectively. We would love to have your feedback!--force_sratools_download
parameter has been deprecated in favour of using --download_method <method>
to explicitly specify the download method; available options are ftp
, sratools
or aspera
.Special thanks to the following for their contributions to the release:
Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.
export CONDA_PREFIX
into container when using Singularity and ApptainerDependency | Old version | New version |
---|---|---|
wget |
1.20.1 |
NB: Dependency has been updated if both old and new version information is present.
NB: Dependency has been added if just the new version information is present.
NB: Dependency has been removed if new version information isn't present.
Old parameter | New parameter |
---|---|
--download_method |
|
--input_type |
|
--force_sratools_download |
|
--synapse_config |
NB: Parameter has been updated if both old and new parameter information is present. NB: Parameter has been added if just the new parameter information is present. NB: Parameter has been removed if new parameter information isn't present.
Full Changelog: https://github.com/nf-core/fetchngs/compare/1.10.1...1.11.0
Special thanks to the following for their contributions to the release:
Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.
public_aws_ecr profile
Dependency | Old version | New version |
---|---|---|
sra-tools |
2.11.0 | 3.0.8 |
NB: Dependency has been updated if both old and new version information is present.
NB: Dependency has been added if just the new version information is present.
NB: Dependency has been removed if new version information isn't present.
Special thanks to the following for their contributions to the release:
Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.
public_aws_ecr.config
to source mulled containers when using public.ecr.aws
Docker Biocontainer registryDependency | Old version | New version |
---|---|---|
synapseclient |
2.6.0 | 2.7.1 |
NB: Dependency has been updated if both old and new version information is present.
NB: Dependency has been added if just the new version information is present.
NB: Dependency has been removed if new version information isn't present.
21.10.3
-> 22.10.1
--nf_core_rnaseq_strandedness
parameter to specify value for strandedness
entry added to samplesheet created when using --nf_core_pipeline rnaseq
. The default is auto
which can be used with nf-core/rnaseq v3.10 onwards to auto-detect strandedness during the pipeline execution.--skip_fastq_download
is provided--force_sratools_download
results in different fastq names compared to FTP downloadtower.yml
to render samplesheet as Report in TowerSRR
and DRR
metadata from ENA API instead of NCBI API to bypass frequent breaking changesSupport for GEO ids has been dropped in this release due to breaking changes introduced in the NCBI API. For more detailed information please see this PR.
As a workaround, if you have a GEO accession you can directly download a text file containing the appropriate SRA ids to pass to the pipeline:
SRA Run Selector
at the bottom of the GEO accession pageSRA Run Selector
and then download the Accession List
This downloads a text file called SRR_Acc_List.txt
that can be directly provided to the pipeline e.g. --input SRR_Acc_List.txt
.
publish_dir_mode
parameter.Dependency | Old version | New version |
---|---|---|
synapseclient |
2.4.0 | 2.6.0 |
21.04.0
-> 21.10.3
--publish_dir_mode
as it is no longer required for the new syntaxsra-tools
.--force_sratools_download
parameter to preferentially download all FastQ files via sra-tools
instead of ENA FTP.{EXP_ACC}_{RUN_ACC}*fastq.gz
instead of {EXP_ACC}_{T*}*fastq.gz
for run id provenanceDDBJ |
---|
PRJDB4176 |
SAMD00114846 |
DRA008156 |
DRP004793 |
DRR171822 |
DRS090921 |
DRX162434 |