Lance Parsons

Uncaught TypeError: Cannot read property 'collectOptions' of undefined

3

[Enter steps to reproduce below:] 1. Open tab separated file in table editor 2. Close atom 3. Reopen and have atom automatically open the file in table editor **Atom Version**:...

Seems like a re-occurance of #16 1. Open file with no headers in tablr 2. Edit header name of one column **Atom**: 1.14.4 x64 **Electron**: 1.3.13 **OS**: Mac OS X...

Snakemake wrappers require cluster nodes to contact github

10

**Snakemake version** 6.6.1 and 6.7.0 **Describe the bug** When attempting to execute workflows with rules that use a snakemake wrapper, the jobs themselves (running on the cluster nodes) attempt to...

Fix bam sort in bismark_wrapper.py

7

Attempting to sort the output bam by position resulted in a samtools error. This commit adds a test for the sort_bam option and fixes the samtools call. Fixes #1033

When attempting to sort a bam file in the bismark bowtie2 tool, (the `sort_bam` option), the following error occurs: ``` Sorting bam with: '['samtools', 'sort', '-@', '6', '/scratch/tmp/galaxy/tmpea26s8rq/results/Trim_Galore__on_data_2_and_data_1__trimmed_reads_pair_1_1_bismark_bt2_pe.bam', 'sorted_bam']' [bam_sort]...

Salmon - Alignment-based mode

4

It would be nice to support Salmon's [alignment-based mode](http://salmon.readthedocs.io/en/latest/salmon.html#alignment-based-mode) for quanitificaton from a BAM file. Are there any plans for this, or any thoughts on how to implement? Same tool...

DeadlockException incorrectly thrown using SLURM

1

I seem to have problems with a Deadlock Exception being thrown when running cactus workflows on our shared SLURM cluster (see https://github.com/ComparativeGenomicsToolkit/cactus/issues/78). I believe that somehow toil isn't capturing the...

"stable" tag on readthedocs does not display the "Code" blocks

1

**Snakemake version** Stable release of wrappers - `0.66.0` **Describe the bug** When viewing the documentation on readthedocs, the `stable` tag doesn't show the `code` blocks. Other version tags and the...

When marking peak groups as good/bad in a peak table, El-MAVEN highlights the background of the group number column a shade of red depending on the fraction of samples with...

Bookmarking - double click vs mark as good or bad

1

When adding bookmark via double click, the bookmark gets added with additional isotope information, however, adding a bookmark by marking as "good" does not seem to add additional isotopic detail....