diff --git a/doc-environment.yml b/doc-environment.yml index 567462063..97191f947 100644 --- a/doc-environment.yml +++ b/doc-environment.yml @@ -13,6 +13,7 @@ dependencies: - jsonschema - gitpython - sphinx + - pip - pip: - sphinxcontrib-napoleon - sphinx-argparse diff --git a/docs/tutorial/basics.rst b/docs/tutorial/basics.rst index d20590138..a0443b28d 100644 --- a/docs/tutorial/basics.rst +++ b/docs/tutorial/basics.rst @@ -360,6 +360,13 @@ But for now, this is enough so that we can add the following rule to our Snakefi "samtools mpileup -g -f {input.fa} {input.bam} | " "bcftools call -mv - > {output}" +With multiple input or output files, it is sometimes handy to refer to them separately in the shell command. +This can be done by **specifying names for input or output files**, for example with ``fa=...``. +The files can then be referred to in the shell command by name, for example with ``{input.fa}``. +For **long shell commands** like this one, it is advisable to **split the string over multiple indented lines**. +Python will automatically merge it into one. +Further, you will notice that the **input or output file lists can contain arbitrary Python statements**, as long as it returns a string, or a list of strings. +Here, we invoke our ``expand`` function to aggregate over the aligned reads of all samples. .. sidebar:: Note @@ -374,16 +381,6 @@ But for now, this is enough so that we can add the following rule to our Snakefi This would concatenate to the command ``"samtools mpileup-g -f {input.fa} {input.bam}"`` and consequently throw the error: ``[main] unrecognized command 'mpileup-g'``. - -With multiple input or output files, it is sometimes handy to refer to them separately in the shell command. -This can be done by **specifying names for input or output files**, for example with ``fa=...``. -The files can then be referred to in the shell command by name, for example with ``{input.fa}``. -For **long shell commands** like this one, it is advisable to **split the string over multiple indented lines**. -Python will automatically merge it into one. -Further, you will notice that the **input or output file lists can contain arbitrary Python statements**, as long as it returns a string, or a list of strings. -Here, we invoke our ``expand`` function to aggregate over the aligned reads of all samples. - - Exercise ........