:::danger
**Disclaimer:** The purpose of the `transit` server is to transfer files to/from the `wharf` area in your sensiteve project. This tutorial is not an official documentation and does not give a guarantee that it will work for any case. If you experience problems following this material - please apply for small project on Rackham/Pelle and use Rackham/Pelle for this purpose.
:::
:::warning
Keep in mind that your $HOME folder is a read-only snapshot of your Rackham/Pelle $HOME folder and has limit of 1.3GB write overlayer.
```
df -h | grep $USER
overlay 1.3G 4.0K 1.3G 1% /domus/h1/XXXXX
```
:::
> This documentation is an adaptation of the original `nf-core` instructions on how to run `nextflow` pipelines OFFLINE.
> https://nf-co.re/docs/usage/getting_started/offline
1. Login to `transit.uppmax.uu.se`
Documentation:
- https://uppmax.github.io/UPPMAX-documentation/cluster_guides/transfer_bianca/#transit-server
2. Mount the `wharf` of your project.
:::: warning
Please, change the project folder `sens2023531` in the instructions bellow to match with your project.
::::
```bash
user@transit:~$ mount_wharf sens2023531
Mounting wharf (accessible for you only) to /home/<user>/sens2023531
Password:
Second factor (TOTP UPPMAX):
done.
```
3. Navigate to your `wharf` folder
```bash
cd sens2023531
```
4. Redirect Apptainer TMPDIR and CACHE to wharf
```bash
export APPTAINER_CACHEDIR=$HOME/sens2023531/APPTAINER_CACHE
export APPTAINER_TMPDIR=$HOME/sens2023531/APPTAINER_TMP
mkdir -p $APPTAINER_CACHEDIR $APPTAINER_TMPDIR
```
5. Load nf-core software module
```bash
ml uppmax git bioinfo-tools nf-core/latest
unset ${!NXF_*}
```
6. Run `nf-core` to download the pipeline.
```bash
nf-core pipelines download -c yes ampliseq
,--./,-.
___ __ __ __ ___ /,-._.--~\
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/tools version 3.0.2 - https://nf-co.re
WARNING Could not find GitHub authentication token. Some API requests may fail.
? Select release / branch: 2.11.0 [release]
In addition to the pipeline code, this tool can download software containers.
? Download software container images: singularity
Nextflow and nf-core can use an environment variable called $NXF_SINGULARITY_CACHEDIR that is a path to a directory where remote
Singularity images are stored. This allows downloaded images to be cached in a central location.
? Define $NXF_SINGULARITY_CACHEDIR for a shared Singularity image download folder? [y/n]: n
If transferring the downloaded files to another system, it can be convenient to have everything compressed in a single file.
This is not recommended when downloading Singularity images, as it can take a long time and saves very little space.
? Choose compression type: none
INFO Saving 'nf-core/ampliseq'
Pipeline revision: '2.11.0'
Use containers: 'singularity'
Container library: 'quay.io'
Output directory: 'nf-core-ampliseq_2.11.0'
Include default institutional configuration: 'True'
INFO Downloading centralised configs from GitHub
INFO Downloading workflow files from GitHub
INFO Processing workflow revision 2.11.0, found 30 container images in total.
...
```
7. Taking care of plugins
Most official plugins are available from the module system on Bianaca. In case something is missing...
https://www.nextflow.io/docs/latest/plugins.html#offline-usage
8. Running on Bianca
```bash
module load bioinfo-tools Nextflow/latest
export NXF_OFFLINE=TRUE
export NXF_OPTS='-Xms1g -Xmx4g' # this is suggested for this particular pipeline
export NXF_SINGULARITY_CACHEDIR=/crex/proj/sens-XXXX-XX/nf-core-ampliseq_2.11.0/singularity-images
nextflow run nf-core-ampliseq_2.11.0/2_11_0/main.nf -profile uppmax --project sens-XXXX-XX --outdir ./results ...
```
:::spoiler Example local run i.e. without SLURM
```
nextflow run nf-core-ampliseq_2.11.0/2_11_0/main.nf -profile singularity --FW_primer "GTGYCAGCMGCCGCGGTAA" --RV_primer "GGACTACNVGGGTWTCTAAT" --input "./nf-core-ampliseq_2.11.0/2_11_0/assets/samplesheet.tsv" --outdir ./results
N E X T F L O W ~ version 24.10.0
Launching `nf-core-ampliseq_2.11.0/2_11_0/main.nf` [magical_rubens] DSL2 - revision: ce811bec9b
WARN: No DADA2 cutoffs were specified (`--trunclenf` & `--trunclenr`), therefore reads will be truncated where median quality drops below 25 (defined by `--trunc_qmin`) but at least a fraction of 0.75 (defined by `--trunc_rmin`) of the reads will be retained.
The chosen cutoffs do not account for required overlap for merging, therefore DADA2 might have poor merging efficiency or even fail.
WARN: Access to undefined parameter `monochromeLogs` -- Initialise it to a default value eg. `params.monochromeLogs = some_value`
------------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/ampliseq v2.11.0
------------------------------------------------------
Core Nextflow options
runName : magical_rubens
containerEngine : singularity
launchDir : /crex/proj/staff/pmitev/nobackup/RT-support/RT-2024.11.08-293532-amliseq
workDir : /crex/proj/staff/pmitev/nobackup/RT-support/RT-2024.11.08-293532-amliseq/work
projectDir : /crex/proj/staff/pmitev/nobackup/RT-support/RT-2024.11.08-293532-amliseq/nf-core-ampliseq_2.11.0/2_11_0
userName : pmitev
profile : singularity
configFiles :
Main arguments
input : ./nf-core-ampliseq_2.11.0/2_11_0/assets/samplesheet.tsv
FW_primer : GTGYCAGCMGCCGCGGTAA
RV_primer : GGACTACNVGGGTWTCTAAT
outdir : ./results
Institutional config options
custom_config_base: /crex/proj/staff/pmitev/nobackup/RT-support/RT-2024.11.08-293532-amliseq/nf-core-ampliseq_2.11.0/2_11_0/../configs/
!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use nf-core/ampliseq for your analysis please cite:
* The pipeline
https://doi.org/10.5281/zenodo.1493841
https://doi.org/10.3389/fmicb.2020.550420
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
https://github.com/nf-core/ampliseq/blob/master/CITATIONS.md
------------------------------------------------------
executor > local (19)
[db/c0864c] NFCORE_AMPLISEQ:AMPLISEQ:RENAME_RAW_DATA_FILES (SRR10070132) [100%] 3 of 3 ?
executor > local (19)
[db/c0864c] NFCORE_AMPLISEQ:AMPLISEQ:RENAME_RAW_DATA_FILES (SRR10070132) [100%] 3 of 3 ?
executor > local (51)
[db/c0864c] NFCORE_AMPLISEQ:AMPLISEQ:RENAME_RAW_DATA_FILES (SRR10070132) [100%] 3 of 3 ?
[e4/d62561] NFCORE_AMPLISEQ:AMPLISEQ:FASTQC (SRR10070132) [100%] 3 of 3 ?
[50/dc23ab] NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_BASIC (SRR10070132) [100%] 3 of 3 ?
[cc/20eb15] NFC?_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_SUMMARY_STD (cutadapt_standard) [100%] 1 of 1 ?
[ef/387e6a] NFC?ISEQ:CUTADAPT_WORKFLOW:CUTADAPT_SUMMARY_MERGE (cutadapt_standard_summary.tsv) [100%] 1 of 1 ?
[0c/3d8c0d] NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_QUALITY1 (FW) [100%] 2 of 2 ?
[e9/52aebd] NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:TRUNCLEN (RV) [100%] 2 of 2 ?
[52/c3cbb9] NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_FILTNTRIM (SRR10070130) [100%] 3 of 3 ?
[a1/a70612] NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_QUALITY2 (FW) [100%] 2 of 2 ?
[b4/12f2a2] NFCORE_AMPLISEQ:AMPLISEQ:DADA2_ERR (2) [100%] 2 of 2 ?
[fc/3e2744] NFCORE_AMPLISEQ:AMPLISEQ:DADA2_DENOISING (2) [100%] 2 of 2 ?
[b2/a92089] NFCORE_AMPLISEQ:AMPLISEQ:DADA2_RMCHIMERA (2) [100%] 2 of 2 ?
[5a/5b5583] NFCORE_AMPLISEQ:AMPLISEQ:DADA2_STATS (2) [100%] 2 of 2 ?
[09/691fb6] NFCORE_AMPLISEQ:AMPLISEQ:DADA2_MERGE [100%] 1 of 1 ?
[87/d79ed2] NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_STD (1) [100%] 1 of 1 ?
[cb/51aad3] NFCORE_AMPLISEQ:AMPLISEQ:BARRNAP (ASV_seqs.fasta) [100%] 1 of 1 ?
[66/2c6ea2] NFCORE_AMPLISEQ:AMPLISEQ:BARRNAPSUMMARY [100%] 1 of 1 ?
[d6/7ad11f] NFCORE_AMPLISEQ:AMPLISEQ:FORMAT_TAXONOMY [100%] 1 of 1 ?
[b0/381770] NFC?AMPLISEQ:DADA2_TAXONOMY_WF:DADA2_TAXONOMY (ASV_seqs.fasta,assignTaxonomy.fna) [100%] 1 of 1 ?
[c4/49394a] NFC?Q:AMPLISEQ:DADA2_TAXONOMY_WF:DADA2_ADDSPECIES (ASV_tax.rds,addSpecies.fna.gz) [100%] 1 of 1 ?
[bb/83097f] NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_INASV (ASV_table.tsv) [100%] 1 of 1 ?
[a0/d76587] NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_INSEQ (ASV_seqs.fasta) [100%] 1 of 1 ?
[bc/bc7f98] NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_INTAX (ASV_tax_species.silva_138.tsv) [100%] 1 of 1 ?
[bd/3c02ac] NFC?IME2_TABLEFILTERTAXA (taxa:mitochondria,chloroplast;min-freq:1;min-samples:1) [100%] 1 of 1 ?
[ad/2100a3] NFC?EQ:AMPLISEQ:QIIME2_SEQFILTERTABLE (rep-seqs.qza filter by filtered-table.qza) [100%] 1 of 1 ?
[49/697e7e] NFCORE_AMPLISEQ:AMPLISEQ:FILTER_STATS [100%] 1 of 1 ?
[10/1fb437] NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_FILTERTAXA (1) [100%] 1 of 1 ?
[13/7601fa] NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:QIIME2_EXPORT_ABSOLUTE [100%] 1 of 1 ?
[96/e0d744] NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:QIIME2_EXPORT_RELASV [100%] 1 of 1 ?
[4d/689818] NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:QIIME2_EXPORT_RELTAX [100%] 1 of 1 ?
[- ] NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:COMBINE_TABLE_QIIME2 -
[91/3da5aa] NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:COMBINE_TABLE_DADA2 [100%] 1 of 1 ?
[- ] NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:COMBINE_TABLE_PPLACE -
[- ] NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:COMBINE_TABLE_SINTAX -
[61/88c1cb] NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_BARPLOT (1) [100%] 1 of 1 ?
[- ] NFCORE_AMPLISEQ:AMPLISEQ:METADATA_ALL -
[- ] NFCORE_AMPLISEQ:AMPLISEQ:METADATA_PAIRWISE -
[bf/5c5930] NFCORE_AMPLISEQ:AMPLISEQ:PHYLOSEQ_WORKFLOW:PHYLOSEQ_INASV [100%] 1 of 1 ?
[83/49857b] NFCORE_AMPLISEQ:AMPLISEQ:PHYLOSEQ_WORKFLOW:PHYLOSEQ (dada2) [100%] 1 of 1 ?
[fc/673519] NFCORE_AMPLISEQ:AMPLISEQ:MULTIQC [100%] 1 of 1 ?
[15/6b97d1] NFCORE_AMPLISEQ:AMPLISEQ:SUMMARY_REPORT (1) [100%] 1 of 1 ?
-[nf-core/ampliseq] Pipeline completed successfully-
Completed at: 08-Nov-2024 10:06:16
Duration : 23m 21s
CPU hours : 3.5
Succeeded : 51
```
:::
Note:
- you might need `-c configs/conf/uppmax.config`, make sure you have the file (it is an option to download it during the pipeline download process).
https://github.com/nf-core/configs/blob/master/conf/uppmax.config
https://nf-co.re/configs/uppmax
- Running `-profile test` or some of the examples might (*most often*) require Internet.
## Contacts:
- [Pavlin Mitev](https://katalog.uu.se/profile/?id=N3-1425)
- [UPPMAX](https://www.uppmax.uu.se/)
- [AE@UPPMAX - related documentation](/8sqXISVRRquPDSw9o1DizQ)
###### tags: `UPPMAX`, `nextflow`, `nf-core`, `transit`
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