bounlu

Docker ECS integration fails on EFS mount with multiple named volumes

3

I am using Docker ECS integration to deploy my multi-container docker compose application as described here: https://docs.docker.com/cloud/ecs-integration/ I use these commands: ``` docker context create ecs aws docker context use...

libboost shared library error

11

I installed salmon from conda environment using python3 and got the below error: ``` $ salmon salmon: error while loading shared libraries: libboost_thread.so.1.60.0: cannot open shared object file: No such...

[BUG] Mutect2 fails

4

I run sarek as below: ``` nextflow run nf-core/sarek \ -profile docker \ -dsl1 \ --sentieon \ --step mapping \ --tools tnscope,mutect2,strelka,snpeff,vep \ --input '/Users/omeran/Desktop/aws/sarek/samplesheet.tsv' \ --outdir 's3://omeran/nextflow/sarek/results/' \ -bucket-dir...

Hi, Can we add `title` parameter to `upsetplot` and make it compatible with `ggtitle`? Just like here: https://github.com/hms-dbmi/UpSetR/issues/76 https://github.com/jonocarroll/UpSetR/commit/ea70aa3a70c287822eedd7c88d83d26eaf5f3ee5

Every run I receive the below warning: `WARN: Output channel ch_gene_bed overrides another variable with the same name declared in the script context -- Rename it to avoid possible conflicts`...

MACS2 default peak type

2

Your document says [here](https://github.com/nf-core/atacseq/blob/master/docs/usage.md#--narrow_peak): > MACS2 is run by default with the --broad flag. However, MACS2 document says the opposite [here](https://github.com/macs3-project/MACS/blob/bce60cf0e523dba306b71644c8397341017e0663/bin/macs3): > --broad > If set, MACS will try to...

Add ability to merge FastQs

3

It is desired to merge files from multiple lanes belonging to the same sample. Often the samples are sequenced in multiple lanes and this indeed speeds up the alignment step,...

Broken link

1

Hi, The link to config file for GIS is broken: https://github.com/nf-core/configs/blob/master/docs/gis.md

Add --error and --skipinstalled options for installBioc.r

1

I have some suggestions which will be very helpful when installing packages by using `installBioc.r`. Just like: `install2.r --error --skipinstalled` please also make these options available for `installBioc.r`: `/usr/local/lib/R/site-library/littler/examples/installBioc.r --error...