From: Kyle Meyer <email@example.com> To: Nicholas Knoblauch <firstname.lastname@example.org> Cc: email@example.com Subject: [PATCH] mode: Add "container" and "envmodules" keywords Date: Sun, 01 Nov 2020 15:36:51 -0500 [thread overview] Message-ID: <firstname.lastname@example.org> (raw) In-Reply-To: <CAG8C6oeB0CSQymy=GmrrFJEUvoq0TFUPv-k2SL0w6sTy4M+FNQ@mail.gmail.com> Nicholas Knoblauch writes: > Hi, > It would be great if snakemake-mode could support `envmodules` and > `containers` as top level commands as per > https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html?highlight=envmodules#using-environment-modules > and > https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html?highlight=envmodules#running-jobs-in-containers Sure, thanks for noticing that they're missing. Based on the docs, my understanding is that "envmodules" can only be used within a rule: rule bwa: envmodules: "bio/bwa/0.7.9" [...] On the other hand, it looks like "container" can be used either within a rule or at the top-level. Is that correct? > Also, maybe I should file a separate issue about this (maybe it isn't even > a snakemake-mode question), but is there a way to force the "rule" line to > never indent (even if I hit 'Tab' on that line)? > I consistently run into whitespace issues with org-mode+snakemake-mode. Hmm, not sure. Starting a separate thread with a minimal reproducer would be great. Thanks. -- >8 -- Subject: [PATCH] mode: Add "container" and "envmodules" keywords Register "container" as both a field key and a top-level command because an example of both is present in the Snakemake docs. Reported-by: Nicholas Knoblauch <email@example.com> --- NEWS | 5 +++-- snakemake-mode.el | 3 +++ 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/NEWS b/NEWS index f046551..2743025 100644 --- a/NEWS +++ b/NEWS @@ -2,8 +2,9 @@ NEWS -- history of user-visible changes -*- mode: org; -*- * master (unreleased) -- Additional Snakemake keywords are now recognized: 'envvars' (new in - Snakemake v5.11.0) and 'cache' keyword (new in v5.12.0). +- Additional Snakemake keywords are now recognized: 'envmodules' (new + in Snakemake v5.9.0), 'envvars' (new in v5.11.0), 'container' (new + in v5.11.0), and 'cache' (new in v5.12.0). * v1.7.0 diff --git a/snakemake-mode.el b/snakemake-mode.el index 5f603ee..cc4d372 100644 --- a/snakemake-mode.el +++ b/snakemake-mode.el @@ -85,7 +85,9 @@ (eval-and-compile (or "benchmark" "cache" "conda" + "container" "cwl" + "envmodules" "group" "input" "log" @@ -110,6 +112,7 @@ (eval-and-compile symbol-end)) (sm-command . ,(rx symbol-start (or "configfile" + "container" "envvars" "include" "localrules" base-commit: 870e1f2379110e48c7f189832aa7663fcb0be836 -- 2.28.0
next prev parent reply other threads:[~2020-11-01 20:36 UTC|newest] Thread overview: 4+ messages / expand[flat|nested] mbox.gz Atom feed top 2020-11-01 19:18 Add 'envmodules' and 'containers' to list of top level commands Nicholas Knoblauch 2020-11-01 20:36 ` Kyle Meyer [this message] 2020-11-01 21:04 ` [PATCH] mode: Add "container" and "envmodules" keywords Nicholas Knoblauch 2020-11-01 21:13 ` Kyle Meyer
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